NM_020402.4:c.62-246G>A

Variant names:

• chr11-3670187-C-T
• rs2672213
• NM_020402.4:c.62-246G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020402.4(CHRNA10):​c.62-246G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,218 control chromosomes in the GnomAD database, including 1,327 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 0.13 (1327 hom., cov: 32)
• Consequence: CHRNA10 NM_020402.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871
• Publications: 5 publications found

Genes affected

CHRNA10 (HGNC:13800): (cholinergic receptor nicotinic alpha 10 subunit) Predicted to enable acetylcholine-gated cation-selective channel activity. Acts upstream of or within positive regulation of cytosolic calcium ion concentration. Predicted to be located in membrane. Predicted to be active in cholinergic synapse and neuron projection. Predicted to be integral component of postsynaptic specialization membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHRNA10	NM_020402.4	c.62-246G>A		intron_variant	Intron 1 of 4	ENST00000250699.2	NP_065135.2
CHRNA10	NM_001303034.2	c.-619-246G>A		intron_variant	Intron 1 of 4		NP_001289963.1
CHRNA10	NM_001303035.2	c.-552-313G>A		intron_variant	Intron 1 of 4		NP_001289964.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHRNA10	ENST00000250699.2	c.62-246G>A		intron_variant	Intron 1 of 4	1	NM_020402.4	ENSP00000250699.2
CHRNA10	ENST00000534359.1	c.-481-313G>A		intron_variant	Intron 1 of 4	1		ENSP00000437107.1
CHRNA10	ENST00000526599.1	n.62-246G>A		intron_variant	Intron 1 of 4	1		ENSP00000432757.1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19426 AN: 152100 Hom.: 1327 Cov.: 32

Gnomad AFR AF: 0.0666

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.128 AC: 19438 AN: 152218 Hom.: 1327 Cov.: 32 AF XY: 0.127 AC XY: 9423 AN XY: 74430

African (AFR) AF: 0.0666 AC: 2765 AN: 41534

American (AMR) AF: 0.162 AC: 2474 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3468

East Asian (EAS) AF: 0.0313 AC: 162 AN: 5174

South Asian (SAS) AF: 0.109 AC: 527 AN: 4820

European-Finnish (FIN) AF: 0.128 AC: 1355 AN: 10620

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.160 AC: 10879 AN: 67992

Other (OTH) AF: 0.171 AC: 361 AN: 2114

Alfa AF: 0.156 Hom.: 3469

Bravo AF: 0.130

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.0
DANN	Benign	0.32
PhyloP100		0.87
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: rs2672213; hg19: chr11-3691417;