12:103234177:C/T
GRCh37/hg19 position 12:103234177
GRCh38/hg38 position 12:102840399
Alleles (ref/alt) C/T
dbSNP rsid rs5030861
Gene symbol

PAH

Most severe consequence splice_donor_variant
Flanking sequence CCGAGTGGCCTCGTAAGGTGTAAATTACTTA[C/T]TGTTAATGGAATCAGCCAAAATCTTAAGCTG
HGVS

NM_000277.3:c.1315+1G>A

NM_001354304.2:c.1315+1G>A

Gene annotations
Transcript Gene Exon number Consequence HGVS cDNA HGVS protein Location Protein location
NM_000277.3 PAH - splice_donor_variant c.1315+1G>A - Intron 12
NM_001354304.2 PAH - splice_donor_variant c.1315+1G>A - Intron 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
ExAC ALL 42 121228 0 0.000346
FIN 0 6596 0 0
NFE 40 66664 0 0.000600
EAS 0 8650 0 0
SAS 0 16508 0 0
AFR 2 10404 0 0.000192
AMR 0 11498 0 0
OTH 0 908 0 0
gnomAD genomes ALL 12 30952 0 0.000387697
FIN 0 3492 0 0
NFE 11 15006 0 0.00073304
ASJ 0 302 0 0
EAS 0 1608 0 0
AFR 1 8724 0 0.000114626
AMR 0 838 0 0
OTH 0 982 0 0
gnomAD exomes ALL 96 246188 0 0.000389946
FIN 0 22296 0 0
NFE 92 111696 0 0.000823664
ASJ 0 9850 0 0
EAS 0 17244 0 0
SAS 0 30782 0 0
AFR 2 15302 0 0.000130702
AMR 1 33538 0 2.98169e-05
OTH 1 5480 0 0.000182482
HRC ALL 45 64976 - 0.000692563
Functional predictions
Tool Score Prediction
MutationTaster 1 disease_causing
CADD 3.732707 -
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++ 5.33 Conserved
phastCons46way primates 0.591 Conserved
phastCons46way placental 0.996 Highly conserved
phastCons100way vertebrates 1.000 Highly conserved
phyloP46way primates 0.561 Conserved
phyloP46way placental 2.664 Conserved
phyloP100way vertebrates 7.049 Conserved
ClinVar
Accession Clinical significance Date last evaluated Review status Method Disease name Disease symbol Disease inheritance Pubmed
RCV000622610 Pathogenic 2021-01-05 criteria provided, single submitter clinical testing Inborn genetic diseases - -

25525159

25087612

3008810

RCV000078510 Pathogenic 2020-04-01 criteria provided, multiple submitters, no conflicts literature only not provided - Autosomal recessive inheritance

2014036

11999982

25087612

22975760

25596310

9634518

23559577

23430918

3615198

23500595

26467025

25525159

3008810

17935162

21228398

RCV000000606 Pathogenic 2018-08-05 reviewed by expert panel clinical testing Phenylketonuria PKU Autosomal recessive inheritance

12655544

3008810

2014036

22526846

24190797

20301677

24941924

17935162

9634518

26542770

3615198

25741868

17576681

25596310

11914042

28492532

9536098

23500595

24368688

17502162

23559577

21228398

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: Pathogenic
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).