12-50080257-T-A

Variant names:

• chr12-50080257-T-A
• rs376184
• NM_001095.4:c.1205+202T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001095.4(ASIC1):​c.1205+202T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ASIC1 NM_001095.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 14 publications found

Genes affected

ASIC1 (HGNC:100): (acid sensing ion channel subunit 1) This gene encodes a member of the acid-sensing ion channel (ASIC) family of proteins, which are part of the degenerin/epithelial sodium channel (DEG/ENaC) superfamily. Members of the ASIC family are sensitive to amiloride and function in neurotransmission. The encoded proteins function in learning, pain transduction, touch sensation, and development of memory and fear. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2012]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001095.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASIC1	NM_001095.4	MANE Select	c.1205+202T>A		intron	N/A	NP_001086.2
	ASIC1	NM_020039.4		c.1205+202T>A		intron	N/A	NP_064423.2
	ASIC1	NM_001256830.2		c.1307+202T>A		intron	N/A	NP_001243759.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASIC1	ENST00000447966.7	TSL:1 MANE Select	c.1205+202T>A		intron	N/A	ENSP00000400228.3
	ASIC1	ENST00000228468.8	TSL:1	c.1205+202T>A		intron	N/A	ENSP00000228468.4
	ASIC1	ENST00000552438.5	TSL:1	c.1307+202T>A		intron	N/A	ENSP00000450247.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 631240 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 328878

African (AFR) AF: 0.00 AC: 0 AN: 15548

American (AMR) AF: 0.00 AC: 0 AN: 19762

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15708

East Asian (EAS) AF: 0.00 AC: 0 AN: 32342

South Asian (SAS) AF: 0.00 AC: 0 AN: 50082

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32218

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2462

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 430846

Other (OTH) AF: 0.00 AC: 0 AN: 32272

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 133415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.75
PhyloP100		-1.4
PromoterAI		0.016	Neutral

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: rs376184; hg19: chr12-50474040;