17-33410403-T-C

Variant names:

• chr17-33410403-T-C
• rs1354492
• ENST00000359872.6:c.556-298336A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000359872.6(ASIC2):​c.556-298336A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,118 control chromosomes in the GnomAD database, including 21,413 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 0.52 (21413 hom., cov: 33)
• Consequence: ASIC2 ENST00000359872.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 8 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASIC2	NM_001094.5	c.556-298336A>G		intron_variant	Intron 1 of 9		NP_001085.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASIC2	ENST00000359872.6	c.556-298336A>G		intron_variant	Intron 1 of 9	1		ENSP00000352934.6

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78698 AN: 152000 Hom.: 21400 Cov.: 33

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.494

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.518 AC: 78756 AN: 152118 Hom.: 21413 Cov.: 33 AF XY: 0.526 AC XY: 39107 AN XY: 74370

African (AFR) AF: 0.362 AC: 15013 AN: 41494

American (AMR) AF: 0.567 AC: 8667 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1748 AN: 3472

East Asian (EAS) AF: 0.845 AC: 4371 AN: 5170

South Asian (SAS) AF: 0.556 AC: 2676 AN: 4810

European-Finnish (FIN) AF: 0.658 AC: 6969 AN: 10588

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37457 AN: 67968

Other (OTH) AF: 0.495 AC: 1045 AN: 2112

Alfa AF: 0.538 Hom.: 100264

Bravo AF: 0.504

Asia WGS AF: 0.645 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1354492; hg19: chr17-31737421;