chr17-33850175-T-G

Variant names:

• chr17-33850175-T-G
• rs317400
• ENST00000359872.6:c.555+305803A>C

Variant summary

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

The ENST00000359872.6(ASIC2):​c.555+305803A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,034 control chromosomes in the GnomAD database, including 5,703 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 0.26 (5703 hom., cov: 32)
• Consequence: ASIC2 ENST00000359872.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000359872.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASIC2	NM_001094.5		c.555+305803A>C		intron	N/A	NP_001085.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASIC2	ENST00000359872.6	TSL:1	c.555+305803A>C		intron	N/A	ENSP00000352934.6
	ENSG00000279668	ENST00000636687.1	TSL:5	n.131-21694A>C		intron	N/A
	ENSG00000279668	ENST00000637947.1	TSL:5	n.87-21694A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40172 AN: 151916 Hom.: 5699 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.264 AC: 40201 AN: 152034 Hom.: 5703 Cov.: 32 AF XY: 0.275 AC XY: 20471 AN XY: 74314

African (AFR) AF: 0.201 AC: 8358 AN: 41482

American (AMR) AF: 0.357 AC: 5452 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3468

East Asian (EAS) AF: 0.490 AC: 2531 AN: 5166

South Asian (SAS) AF: 0.310 AC: 1491 AN: 4806

European-Finnish (FIN) AF: 0.379 AC: 4003 AN: 10570

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17091 AN: 67948

Other (OTH) AF: 0.236 AC: 498 AN: 2110

Alfa AF: 0.240 Hom.: 2565

Bravo AF: 0.262

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.47
PhyloP100		0.25
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: rs317400; hg19: chr17-32177194;