rs9891330

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000583224.3(ENSG00000263571):​n.1137+1079G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 147,662 control chromosomes in the GnomAD database, including 10,718 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 0.38 ( 10718 hom., cov: 30)

Consequence


ENST00000583224.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.35
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000583224.3 linkuse as main transcriptn.1137+1079G>C intron_variant, non_coding_transcript_variant 5
ASIC2ENST00000583395.1 linkuse as main transcriptn.406-498C>G intron_variant, non_coding_transcript_variant 2
ENST00000667899.1 linkuse as main transcriptn.1089+1079G>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.381
AC:
56193
AN:
147548
Hom.:
10711
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.352
Gnomad AMI
AF:
0.364
Gnomad AMR
AF:
0.341
Gnomad ASJ
AF:
0.501
Gnomad EAS
AF:
0.193
Gnomad SAS
AF:
0.366
Gnomad FIN
AF:
0.393
Gnomad MID
AF:
0.497
Gnomad NFE
AF:
0.414
Gnomad OTH
AF:
0.414
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.381
AC:
56226
AN:
147662
Hom.:
10718
Cov.:
30
AF XY:
0.378
AC XY:
27296
AN XY:
72170
show subpopulations
Gnomad4 AFR
AF:
0.352
Gnomad4 AMR
AF:
0.341
Gnomad4 ASJ
AF:
0.501
Gnomad4 EAS
AF:
0.192
Gnomad4 SAS
AF:
0.366
Gnomad4 FIN
AF:
0.393
Gnomad4 NFE
AF:
0.414
Gnomad4 OTH
AF:
0.411
Alfa
AF:
0.404
Hom.:
1188
Bravo
AF:
0.383
Asia WGS
AF:
0.252
AC:
788
AN:
3120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.5
DANN
Benign
0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9891330; hg19: chr17-32484800; API