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10:43597793:G/A
GRCh37/hg19 position 10:43597793
GRCh38/hg38 position 10:43102345
Alleles (ref/alt) G/A
dbSNP rsid rs76397662
Gene symbol

RET
Most severe consequence missense_variant
Flanking sequence CCCCCACAGACCTGACTTCTCTCTGCAGACC[G/A]CGGCTTTCCCCTGCTCACCGTCTACCTCAAG
HGVS

NM_020630.6:c.341G>A

NM_020975.6:c.341G>A

NP_065681.1:p.Arg114His

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Gene annotations
Transcript Gene Exon number Consequence HGVS cDNA HGVS protein Location Protein location
NM_001355216.1 RET - upstream_gene_variant - - 2387 bp to transcript
NM_020630.6 RET 19 missense_variant c.341G>A p.Arg114His Exon 3
NM_020975.6 RET 20 missense_variant c.341G>A p.Arg114His Exon 3
Population frequency
Select populations: ALL LWK MKK YRI EUR FIN NFE CEU ASJ TSI EAS SAS CHB HAN CHD JPT AFR AMR ASW GIH MEX OTH
Database Population AC AN Hom AF
1000 genomes ALL 7 5008 - 0.00139776
EUR - - - 0
EAS - - - 0.006
SAS - - - 0.001
AFR - - - 0
AMR - - - 0
ExAC ALL 107 121326 1 0.000882
FIN 0 6614 0 0
NFE 7 66686 0 0.000105
EAS 98 8652 1 0.011327
SAS 2 16512 0 0.000121
AFR 0 10386 0 0
AMR 0 11570 0 0
OTH 0 906 0 0
gnomAD genomes ALL 24 30946 0 0.000775544
FIN 0 3492 0 0
NFE 2 14988 0 0.00013344
ASJ 0 302 0 0
EAS 22 1620 0 0.0135802
AFR 0 8724 0 0
AMR 0 838 0 0
OTH 0 982 0 0
gnomAD exomes ALL 188 245144 0 0.000766896
FIN 0 22094 0 0
NFE 7 110828 0 6.31609e-05
ASJ 0 9842 0 0
EAS 175 17248 0 0.0101461
SAS 6 30780 0 0.000194932
AFR 0 15304 0 0
AMR 0 33578 0 0
OTH 0 5470 0 0
CONVERGE ALL - - - 0.008
HRC ALL 9 64976 - 0.000138513
Functional predictions
Tool Score Prediction
SIFT 0.157 tolerated
Polyphen2 HDIV 0.007 benign
Polyphen2 HVAR 0.002 benign
LRT 0.116724 neutral
MutationTaster 0.00621181 disease_causing_automatic
MutationAssessor 0 neutral
FATHMM -1.2 tolerated
MetaSVM -0.6502 tolerated
MetaLR 0.1718 tolerated
PROVEAN -0.99 neutral
CADD 1.862061 -
REVEL 0.419 -
Conservation
Conservation scores are retrieved from UCSC genome browser. The conservation levels are defined by simple cutoff values. If the conservation levels do not agree with each other, you can manually check whether this variant is conserved with UCSC genome browser.
Method Score Level
GERP++ 4.82 Conserved
phastCons46way primates 0.010 Not conserved
phastCons46way placental 0.587 Conserved
phastCons100way vertebrates 0.653 Conserved
phyloP46way primates 0.655 Conserved
phyloP46way placental 2.214 Conserved
phyloP100way vertebrates 2.402 Not conserved
ClinVar
Accession Clinical significance Date last evaluated Review status Method Disease name Disease symbol Disease inheritance Pubmed
RCV000014974 Uncertain significance 2002-04-01 no assertion criteria provided literature only Congenital central hypoventilation - -

12086152
RCV000163885 Benign 2020-04-28 criteria provided, multiple submitters, no conflicts curation Hereditary cancer-predisposing syndrome - -

24728327

22174939

12086152

20473317

14633923

20532249

23084198
RCV001106779 Benign 2017-04-28 criteria provided, single submitter clinical testing Multiple endocrine neoplasia - - -
RCV000755684 Benign 2018-11-21 criteria provided, single submitter clinical testing Multiple endocrine neoplasia type 2B - -

25741868
RCV003389668 Likely benign 2023-08-01 criteria provided, single submitter clinical testing not provided - - -
RCV001106778 Likely benign 2017-04-28 criteria provided, single submitter clinical testing Renal hypodysplasia/aplasia 1 RHDA1 - -
RCV000121988 Benign 2017-01-05 criteria provided, single submitter reference population not specified - -

24728327
RCV004739309 Uncertain significance 2024-04-05 no assertion criteria provided clinical testing RET-related disorder - - -
RCV001107412 Benign 2017-04-28 criteria provided, single submitter clinical testing Pheochromocytoma - - -
RCV000490359 Benign 2016-03-18 criteria provided, single submitter reference population Hirschsprung disease, susceptibility to, 1 - -

20473317

25741868

12086152
RCV000198261 Benign 2025-02-03 criteria provided, single submitter clinical testing Multiple endocrine neoplasia, type 2 MEN2 -

28492532
InterVar

InterVar is a software tool for clinical interpretation of genetic variants by the ACMG/AMP 2015 guideline. The eveidence tags that variant met are highlighted. Please note that evidence tags with need to be evaluated manually.

Class: Benign
Benign Pathogenic
Strong Supporting Supporting Moderate Strong Very Strong
Population data BA1
BS1
BS2 		PM2 PS4
Computational and predictive data BP1
BP3
BP4
BP7 		PP3 PM4
PM5		 PS1 PVS1
Functional data BS3 PP2 PM1 PS3
Segregation data BS4 PP1 PP1 PP1
De novo data PM6 PS2
Allelic data BP2 PM3
Other database BP6 PP5
Other data BP5 PP4
Amino acid change

The physichemical property of amino acid change.

Trait Arg (R) His (H)
Amino acid name Arginine Histidine
Side chain class basic basic aromatic
Polarity basic polar basic polar
Charge (pH=7.4) positively charged positively or neutrally charged
Hydropathy hydrophilic moderate
Molecular weight 174.203 155.156
gnomAD
The Genome Aggregation Database (gnomAD), is a coalition of investigators seeking to aggregate and harmonize exome and genome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. In its first release, which contained exclusively exome data, it was known as the Exome Aggregation Consortium (ExAC).