chr17-33078063-G-A

Variant names:

• chr17-33078063-G-A
• rs12451625
• NM_183377.2:c.987+10800C>T

Variant summary

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

The NM_183377.2(ASIC2):​c.987+10800C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,072 control chromosomes in the GnomAD database, including 912 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 0.10 (912 hom., cov: 32)
• Consequence: ASIC2 NM_183377.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASIC2	NM_183377.2	c.987+10800C>T		intron_variant	Intron 3 of 9	ENST00000225823.7	NP_899233.1
ASIC2	NM_001094.5	c.834+10800C>T		intron_variant	Intron 3 of 9		NP_001085.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASIC2	ENST00000225823.7	c.987+10800C>T		intron_variant	Intron 3 of 9	1	NM_183377.2	ENSP00000225823.2
ASIC2	ENST00000359872.6	c.834+10800C>T		intron_variant	Intron 3 of 9	1		ENSP00000352934.6
ASIC2	ENST00000448983.1	n.392+10800C>T		intron_variant	Intron 4 of 6	3

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15587 AN: 151954 Hom.: 907 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.0319

Gnomad SAS AF: 0.0457

Gnomad FIN AF: 0.0454

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0893

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.103 AC: 15599 AN: 152072 Hom.: 912 Cov.: 32 AF XY: 0.0997 AC XY: 7412 AN XY: 74352

African (AFR) AF: 0.156 AC: 6465 AN: 41470

American (AMR) AF: 0.0922 AC: 1409 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0980 AC: 340 AN: 3468

East Asian (EAS) AF: 0.0317 AC: 164 AN: 5168

South Asian (SAS) AF: 0.0459 AC: 221 AN: 4810

European-Finnish (FIN) AF: 0.0454 AC: 480 AN: 10572

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0893 AC: 6071 AN: 67988

Other (OTH) AF: 0.107 AC: 227 AN: 2112

Alfa AF: 0.0958 Hom.: 217

Bravo AF: 0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.067
DANN	Benign	0.64
PhyloP100		-2.2
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: rs12451625; hg19: chr17-31405081;