rs1376866

Positions:

• chr2-174763128-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000079.4(CHRNA1):​c.43+1224G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,082 control chromosomes in the GnomAD database, including 45,490 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 0.75 (45490 hom., cov: 32)
• Consequence: CHRNA1 NM_000079.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHRNA1	NM_000079.4	c.43+1224G>A		intron_variant		ENST00000348749.9	NP_000070.1
CHRNA1	NM_001039523.3	c.43+1224G>A		intron_variant			NP_001034612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHRNA1	ENST00000348749.9	c.43+1224G>A		intron_variant		1	NM_000079.4	ENSP00000261008	P1
	ENST00000442996.1	n.322-9621C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113523 AN: 151964 Hom.: 45494 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.747 AC: 113545 AN: 152082 Hom.: 45490 Cov.: 32 AF XY: 0.752 AC XY: 55905 AN XY: 74356

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.761

Alfa AF: 0.833 Hom.: 25025

Bravo AF: 0.730

Asia WGS AF: 0.761 AC: 2648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs1376866; hg19: chr2-175627856;