chr17-33413163-G-A
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000359872.6(ASIC2):c.556-301096C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,034 control chromosomes in the GnomAD database, including 6,738 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.27 ( 6738 hom., cov: 32)
Consequence
ASIC2
ENST00000359872.6 intron
ENST00000359872.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.936
Publications
5 publications found
Genes affected
ASIC2 (HGNC:99): (acid sensing ion channel subunit 2) This gene encodes a member of the degenerin/epithelial sodium channel (DEG/ENaC) superfamily. The members of this family are amiloride-sensitive sodium channels that contain intracellular N and C termini, 2 hydrophobic transmembrane regions, and a large extracellular loop, which has many cysteine residues with conserved spacing. The member encoded by this gene may play a role in neurotransmission. In addition, a heteromeric association between this member and acid-sensing (proton-gated) ion channel 3 has been observed to co-assemble into proton-gated channels sensitive to gadolinium. Alternative splicing has been observed at this locus and two variants, encoding distinct isoforms, have been identified. [provided by RefSeq, Feb 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.266 AC: 40389AN: 151916Hom.: 6740 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
40389
AN:
151916
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.266 AC: 40390AN: 152034Hom.: 6738 Cov.: 32 AF XY: 0.268 AC XY: 19885AN XY: 74280 show subpopulations
GnomAD4 genome
AF:
AC:
40390
AN:
152034
Hom.:
Cov.:
32
AF XY:
AC XY:
19885
AN XY:
74280
show subpopulations
African (AFR)
AF:
AC:
2755
AN:
41508
American (AMR)
AF:
AC:
4396
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
880
AN:
3470
East Asian (EAS)
AF:
AC:
944
AN:
5156
South Asian (SAS)
AF:
AC:
1500
AN:
4804
European-Finnish (FIN)
AF:
AC:
4390
AN:
10552
Middle Eastern (MID)
AF:
AC:
85
AN:
292
European-Non Finnish (NFE)
AF:
AC:
24428
AN:
67952
Other (OTH)
AF:
AC:
556
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1396
2792
4189
5585
6981
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
426
852
1278
1704
2130
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
677
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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