rs725276

Variant names:

• chr17-33546362-T-A
• rs725276
• ENST00000359872.6:c.556-434295A>T

Your query was ambiguous. Multiple possible variants found:

• chr17-33546362-T-A
• chr17-33546362-T-C

Variant summary

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

The NM_001094.5(ASIC2):​c.556-434295A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,794 control chromosomes in the GnomAD database, including 16,349 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 0.46 (16349 hom., cov: 31)
• Consequence: ASIC2 NM_001094.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 1 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]

ENSG00000265125 (HGNC:27103):

LOC112268206 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001094.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASIC2	NM_001094.5		c.556-434295A>T		intron	N/A	NP_001085.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASIC2	ENST00000359872.6	TSL:1	c.556-434295A>T		intron	N/A	ENSP00000352934.6	Q16515-1
	ENSG00000265125	ENST00000726249.1		n.139-421T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70233 AN: 151676 Hom.: 16349 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.463 AC: 70270 AN: 151794 Hom.: 16349 Cov.: 31 AF XY: 0.466 AC XY: 34541 AN XY: 74158

African (AFR) AF: 0.449 AC: 18577 AN: 41372

American (AMR) AF: 0.452 AC: 6889 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1750 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1548 AN: 5148

South Asian (SAS) AF: 0.533 AC: 2565 AN: 4814

European-Finnish (FIN) AF: 0.537 AC: 5648 AN: 10518

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31814 AN: 67928

Other (OTH) AF: 0.462 AC: 973 AN: 2106

Alfa AF: 0.459 Hom.: 2025

Bravo AF: 0.452

Asia WGS AF: 0.439 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.69
PhyloP100		-0.030
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: rs725276; hg19: chr17-31873381;