ENST00000359872.6:c.555+174062C>T

Variant names:

• chr17-33981916-G-A
• rs4794984
• ENST00000359872.6:c.555+174062C>T

Variant summary

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

The ENST00000359872.6(ASIC2):​c.555+174062C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,178 control chromosomes in the GnomAD database, including 1,478 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 0.12 (1478 hom., cov: 32)
• Consequence: ASIC2 ENST00000359872.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 3 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]

ENSG00000279668 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASIC2	NM_001094.5	c.555+174062C>T		intron_variant	Intron 1 of 9		NP_001085.2
LOC107985038	XR_001752840.2	n.221+5229C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASIC2	ENST00000359872.6	c.555+174062C>T		intron_variant	Intron 1 of 9	1		ENSP00000352934.6
ENSG00000279668	ENST00000584758.2	n.188+2271C>T		intron_variant	Intron 1 of 1	5
ENSG00000265356	ENST00000636421.1	n.459-45094C>T		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18076 AN: 152060 Hom.: 1478 Cov.: 32

Gnomad AFR AF: 0.0285

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.119 AC: 18078 AN: 152178 Hom.: 1478 Cov.: 32 AF XY: 0.122 AC XY: 9080 AN XY: 74380

African (AFR) AF: 0.0284 AC: 1180 AN: 41542

American (AMR) AF: 0.151 AC: 2302 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1789 AN: 5158

South Asian (SAS) AF: 0.145 AC: 698 AN: 4822

European-Finnish (FIN) AF: 0.177 AC: 1875 AN: 10578

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9194 AN: 68006

Other (OTH) AF: 0.140 AC: 295 AN: 2112

Alfa AF: 0.130 Hom.: 244

Bravo AF: 0.116

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.71
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4794984; hg19: chr17-32308935;