chr17-33050525-G-A

Variant names:

• chr17-33050525-G-A
• rs16581
• NM_183377.2:c.988-22133C>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.988-22133C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,066 control chromosomes in the GnomAD database, including 3,432 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 0.18 (3432 hom., cov: 31)
• Consequence: ASIC2 NM_183377.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 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.988-22133C>T		intron	N/A	NP_899233.1	Q16515-2
	ASIC2	NM_001094.5		c.835-22133C>T		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.988-22133C>T		intron	N/A	ENSP00000225823.2	Q16515-2
	ASIC2	ENST00000359872.6	TSL:1	c.835-22133C>T		intron	N/A	ENSP00000352934.6	Q16515-1
	ASIC2	ENST00000448983.1	TSL:3	n.393-22133C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27606 AN: 151948 Hom.: 3417 Cov.: 31

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.182 AC: 27630 AN: 152066 Hom.: 3432 Cov.: 31 AF XY: 0.188 AC XY: 13941 AN XY: 74296

African (AFR) AF: 0.0422 AC: 1753 AN: 41538

American (AMR) AF: 0.272 AC: 4154 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3468

East Asian (EAS) AF: 0.486 AC: 2498 AN: 5142

South Asian (SAS) AF: 0.262 AC: 1263 AN: 4814

European-Finnish (FIN) AF: 0.268 AC: 2831 AN: 10544

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14088 AN: 67968

Other (OTH) AF: 0.170 AC: 358 AN: 2112

Alfa AF: 0.196 Hom.: 11319

Bravo AF: 0.177

Asia WGS AF: 0.337 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.50
PhyloP100		1.4
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: rs16581; hg19: chr17-31377543;