Variant rs2228990 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000359872.6(ASIC2):c.315T>C(p.Asn105=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,613,928 control chromosomes in the GnomAD database, including 38,440 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 0.22 ( 3793 hom., cov: 32)

Exomes 𝑓: 0.21 ( 34647 hom. )

Consequence

ASIC2
ENST00000359872.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.275

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]

ASIC2 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP7

Synonymous conserved (PhyloP=-0.275 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASIC2	NM_001094.5 linkuse as main transcript	c.315T>C	p.Asn105=	synonymous_variant	1/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Appris	UniProt
ASIC2	ENST00000359872.6 linkuse as main transcript	c.315T>C	p.Asn105=	synonymous_variant	1/10	1	P1	Q16515-1
	ENST00000583224.3 linkuse as main transcript	n.653A>G		non_coding_transcript_exon_variant	1/4	5
	ENST00000667899.1 linkuse as main transcript	n.605A>G		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes

AF:

0.215

AC:

32739

AN:

151966

Hom.:

3788

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.353

Gnomad SAS

AF:

0.302

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.178

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.207

GnomAD3 exomes

AF:

0.246

AC:

61499

AN:

249508

Hom.:

8626

AF XY:

0.242

AC XY:

32740

AN XY:

135346

show subpopulations

Gnomad AFR exome

AF:

0.178

Gnomad AMR exome

AF:

0.415

Gnomad ASJ exome

AF:

0.164

Gnomad EAS exome

AF:

0.346

Gnomad SAS exome

AF:

0.289

Gnomad FIN exome

AF:

0.229

Gnomad NFE exome

AF:

0.190

Gnomad OTH exome

AF:

0.210

GnomAD4 exome

AF:

0.210

AC:

307499

AN:

1461842

Hom.:

34647

Cov.:

AF XY:

0.212

AC XY:

153970

AN XY:

727222

show subpopulations

Gnomad4 AFR exome

AF:

0.176

Gnomad4 AMR exome

AF:

0.401

Gnomad4 ASJ exome

AF:

0.168

Gnomad4 EAS exome

AF:

0.340

Gnomad4 SAS exome

AF:

0.288

Gnomad4 FIN exome

AF:

0.229

Gnomad4 NFE exome

AF:

0.193

Gnomad4 OTH exome

AF:

0.215

GnomAD4 genome

AF:

0.215

AC:

32772

AN:

152086

Hom.:

3793

Cov.:

AF XY:

0.222

AC XY:

16502

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.179

Gnomad4 AMR

AF:

0.333

Gnomad4 ASJ

AF:

0.173

Gnomad4 EAS

AF:

0.353

Gnomad4 SAS

AF:

0.302

Gnomad4 FIN

AF:

0.235

Gnomad4 NFE

AF:

0.195

Gnomad4 OTH

AF:

0.210

Alfa

AF:

0.201

Hom.:

2360

Bravo

AF:

0.220

Asia WGS

AF:

0.318

AC:

1106

AN:

3478

EpiCase

AF:

0.198

EpiControl

AF:

0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

4.2

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over