17-33038811-T-C

Variant names:

• chr17-33038811-T-C
• rs16559
• NM_183377.2:c.988-10419A>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.988-10419A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,122 control chromosomes in the GnomAD database, including 53,889 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 0.84 (53889 hom., cov: 31)
• Consequence: ASIC2 NM_183377.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 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.988-10419A>G		intron	N/A	NP_899233.1	Q16515-2
	ASIC2	NM_001094.5		c.835-10419A>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.988-10419A>G		intron	N/A	ENSP00000225823.2	Q16515-2
	ASIC2	ENST00000359872.6	TSL:1	c.835-10419A>G		intron	N/A	ENSP00000352934.6	Q16515-1
	ASIC2	ENST00000448983.1	TSL:3	n.393-10419A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127303 AN: 152004 Hom.: 53825 Cov.: 31

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.838 AC: 127420 AN: 152122 Hom.: 53889 Cov.: 31 AF XY: 0.832 AC XY: 61853 AN XY: 74358

African (AFR) AF: 0.960 AC: 39858 AN: 41508

American (AMR) AF: 0.863 AC: 13202 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2661 AN: 3470

East Asian (EAS) AF: 0.750 AC: 3868 AN: 5160

South Asian (SAS) AF: 0.725 AC: 3491 AN: 4814

European-Finnish (FIN) AF: 0.763 AC: 8067 AN: 10566

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53609 AN: 67984

Other (OTH) AF: 0.814 AC: 1718 AN: 2110

Alfa AF: 0.809 Hom.: 63077

Bravo AF: 0.854

Asia WGS AF: 0.733 AC: 2550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.52
PhyloP100		-1.0
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16559;

hg19: chr17-31365829;