GeneBe

rs3744516

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001094.5(ASIC2):​c.555+116997T>G variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Consequence

ASIC2
NM_001094.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.17
Variant links:
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]
TLK2P1 (HGNC:18048): (tousled like kinase 2 pseudogene 1)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ASIC2NM_001094.5 linkc.555+116997T>G intron_variant Intron 1 of 9 NP_001085.2 Q16515-1
TLK2P1 n.34038981A>C intragenic_variant
LOC107987247XR_002958159.2 linkn.2247+9351T>G intron_variant Intron 4 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ASIC2ENST00000359872.6 linkc.555+116997T>G intron_variant Intron 1 of 9 1 ENSP00000352934.6 Q16515-1
TLK2P1ENST00000530992.1 linkn.892T>G non_coding_transcript_exon_variant Exon 1 of 1 6
ENSG00000265356ENST00000636421.1 linkn.458+2253T>G intron_variant Intron 3 of 3 5

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
51
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
1.8
DANN
Benign
0.64

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3744516; hg19: chr17-32366000; API