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12:103234215:A/G
GRCh37/hg19 position 12:103234215
GRCh38/hg38 position 12:102840437
Alleles (ref/alt) A/G
dbSNP rsid rs59326968
Gene symbol

PAH
Most severe consequence synonymous_variant
Flanking sequence TGGAATCAGCCAAAATCTTAAGCTGCTGGGT[A/G]TTGTCCAAGACCTCAATCCTTTGGGTGTATG
HGVS

NM_000277.3:c.1278T>C

NM_001354304.2:c.1278T>C

NP_000268.1:p.Asn426=

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Gene annotations
Transcript Gene Exon number Consequence HGVS cDNA HGVS protein Location Protein location
NM_000277.3 PAH 13 synonymous_variant c.1278T>C p.Asn426= Exon 12
NM_001354304.2 PAH 14 synonymous_variant c.1278T>C p.Asn426= Exon 13
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 233 5008 - 0.0465256
EUR - - - 0.001
EAS - - - 0
SAS - - - 0
AFR - - - 0.1664
AMR - - - 0.0173
ExAC ALL 1653 121330 104 0.013624
FIN 1 6612 0 0.000151
NFE 33 66714 0 0.000495
EAS 0 8654 0 0
SAS 6 16510 0 0.000363
AFR 1525 10406 104 0.146550
AMR 82 11526 0 0.007114
OTH 6 908 0 0.006608
gnomAD genomes ALL 1258 30958 88 0.0406357
FIN 0 3492 0 0
NFE 9 15008 0 0.00059968
ASJ 0 302 0 0
EAS 0 1618 0 0
AFR 1238 8718 88 0.142005
AMR 4 838 0 0.00477327
OTH 7 982 0 0.00712831
gnomAD exomes ALL 2611 246218 181 0.0106044
FIN 1 22300 0 4.4843e-05
NFE 57 111688 0 0.00051035
ASJ 4 9850 0 0.000406091
EAS 1 17248 0 5.79777e-05
SAS 10 30782 1 0.000324865
AFR 2246 15302 178 0.146778
AMR 255 33564 2 0.00759743
OTH 37 5484 0 0.0067469
HRC ALL 300 64976 - 0.00461709
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++ -3.99 Not conserved
phastCons46way primates 0.981 Highly conserved
phastCons46way placental 0.872 Conserved
phastCons100way vertebrates 0.914 Highly conserved
phyloP46way primates 0.459 Not conserved
phyloP46way placental -0.666 Not conserved
phyloP100way vertebrates 0.063 Not conserved
ClinVar
Accession Clinical significance Date last evaluated Review status Method Disease name Disease symbol Disease inheritance Pubmed
RCV000088823 Benign 2021-01-13 criteria provided, multiple submitters, no conflicts clinical testing not provided - -

11139255

26467025

11180595
RCV000400696 Benign 2018-08-10 reviewed by expert panel curation Phenylketonuria PKU Autosomal recessive inheritance

28492532
RCV000078509 Benign/Likely benign 2012-10-18 criteria provided, multiple submitters, no conflicts clinical testing not specified - -

25741868
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: Likely 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
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).