rs10629807

Positions:

• chr2-174763827-T-TTC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000079.4(CHRNA1):​c.43+524_43+525insGA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.82 (51573 hom., cov: 0)
• Consequence: CHRNA1 NM_000079.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95

Genes affected

CHRNA1 (HGNC:1955): (cholinergic receptor nicotinic alpha 1 subunit) The muscle acetylcholine receptor consiststs of 5 subunits of 4 different types: 2 alpha subunits and 1 each of the beta, gamma, and delta subunits. This gene encodes an alpha subunit that plays a role in acetlycholine binding/channel gating. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Nov 2012]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHRNA1	NM_000079.4	c.43+524_43+525insGA		intron_variant		ENST00000348749.9
CHRNA1	NM_001039523.3	c.43+524_43+525insGA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHRNA1	ENST00000348749.9	c.43+524_43+525insGA		intron_variant		1	NM_000079.4	P1
	ENST00000442996.1	n.322-8921_322-8920insCT		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124032 AN: 151804 Hom.: 51551 Cov.: 0

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.817 AC: 124104 AN: 151922 Hom.: 51573 Cov.: 0 AF XY: 0.820 AC XY: 60895 AN XY: 74250

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.817

Alfa AF: 0.826 Hom.: 5619

Asia WGS AF: 0.801 AC: 2786 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10629807; hg19: chr2-175628555;