rs12910984

Positions:

• chr15-78599285-G-A
• chr15-78599285-G-C
• chr15-78599285-G-T

Variant summary

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

The NM_000743.5(CHRNA3):​c.1389+1968C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,098 control chromosomes in the GnomAD database, including 37,841 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 0.70 (37841 hom., cov: 32)
• Consequence: CHRNA3 NM_000743.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

Genes affected

CHRNA3 (HGNC:1957): (cholinergic receptor nicotinic alpha 3 subunit) This locus encodes a member of the nicotinic acetylcholine receptor family of proteins. Members of this family of proteins form pentameric complexes comprised of both alpha and beta subunits. This locus encodes an alpha-type subunit, as it contains characteristic adjacent cysteine residues. The encoded protein is a ligand-gated ion channel that likely plays a role in neurotransmission. Polymorphisms in this gene have been associated with an increased risk of smoking initiation and an increased susceptibility to lung cancer. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHRNA3	NM_000743.5	c.1389+1968C>T		intron_variant		ENST00000326828.6	NP_000734.2
CHRNA3	NM_001166694.2	c.1389+1968C>T		intron_variant			NP_001160166.1
CHRNA3	XM_006720382.4	c.1188+1968C>T		intron_variant			XP_006720445.1
CHRNA3	NR_046313.2	n.1591+1968C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHRNA3	ENST00000326828.6	c.1389+1968C>T		intron_variant		1	NM_000743.5	ENSP00000315602	P1
CHRNA3	ENST00000348639.7	c.1389+1968C>T		intron_variant		1		ENSP00000267951
CHRNA3	ENST00000559658.5	c.1389+1968C>T		intron_variant, NMD_transcript_variant		2		ENSP00000452896

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106096 AN: 151980 Hom.: 37822 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.698 AC: 106146 AN: 152098 Hom.: 37841 Cov.: 32 AF XY: 0.691 AC XY: 51385 AN XY: 74370

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.687

Alfa AF: 0.728 Hom.: 16577

Bravo AF: 0.683

Asia WGS AF: 0.516 AC: 1796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.75
DANN	Benign	0.23

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: rs12910984; hg19: chr15-78891627;