rs1557753

Variant names:

• chr17-33054800-T-C
• rs1557753
• NM_183377.2:c.988-26408A>G

Variant summary

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

The NM_183377.2(ASIC2):​c.988-26408A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,318 control chromosomes in the GnomAD database, including 64,702 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 0.92 (64702 hom., cov: 34)
• Consequence: ASIC2 NM_183377.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_183377.2. 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_183377.2	MANE Select	c.988-26408A>G		intron	N/A	NP_899233.1	Q16515-2
	ASIC2	NM_001094.5		c.835-26408A>G		intron	N/A	NP_001085.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASIC2	ENST00000225823.7	TSL:1 MANE Select	c.988-26408A>G		intron	N/A	ENSP00000225823.2	Q16515-2
	ASIC2	ENST00000359872.6	TSL:1	c.835-26408A>G		intron	N/A	ENSP00000352934.6	Q16515-1
	ASIC2	ENST00000448983.1	TSL:3	n.393-26408A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140154 AN: 152200 Hom.: 64644 Cov.: 34

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.921 AC: 140271 AN: 152318 Hom.: 64702 Cov.: 34 AF XY: 0.923 AC XY: 68701 AN XY: 74468

African (AFR) AF: 0.977 AC: 40612 AN: 41580

American (AMR) AF: 0.931 AC: 14251 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3120 AN: 3470

East Asian (EAS) AF: 0.964 AC: 4990 AN: 5178

South Asian (SAS) AF: 0.945 AC: 4560 AN: 4824

European-Finnish (FIN) AF: 0.904 AC: 9585 AN: 10602

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60160 AN: 68038

Other (OTH) AF: 0.905 AC: 1915 AN: 2116

Alfa AF: 0.896 Hom.: 37720

Bravo AF: 0.924

Asia WGS AF: 0.955 AC: 3322 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	6.6
DANN	Benign	0.51
PhyloP100		-0.024
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: rs1557753; hg19: chr17-31381818;