rs601079

Variant names:

• chr15-78577237-T-A
• rs601079
• NM_000745.4:c.107-3574T>A

Your query was ambiguous. Multiple possible variants found:

• chr15-78577237-T-A
• chr15-78577237-T-C
• chr15-78577237-T-G

Variant summary

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

The NM_000745.4(CHRNA5):​c.107-3574T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 152,030 control chromosomes in the GnomAD database, including 28,116 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 0.60 (28116 hom., cov: 31)
• Consequence: CHRNA5 NM_000745.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 18 publications found

Genes affected

CHRNA5 (HGNC:1959): (cholinergic receptor nicotinic alpha 5 subunit) The protein encoded by this gene is a nicotinic acetylcholine receptor subunit and a member of a superfamily of ligand-gated ion channels that mediate fast signal transmission at synapses. These receptors are thought to be heteropentamers composed of separate but similar subunits. Defects in this gene have been linked to susceptibility to lung cancer type 2 (LNCR2).[provided by RefSeq, Jun 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHRNA5	NM_000745.4	c.107-3574T>A		intron_variant	Intron 1 of 5	ENST00000299565.9	NP_000736.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHRNA5	ENST00000299565.9	c.107-3574T>A		intron_variant	Intron 1 of 5	1	NM_000745.4	ENSP00000299565.5
CHRNA5	ENST00000559554.5	c.107-3574T>A		intron_variant	Intron 1 of 5	3		ENSP00000453519.1

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91838 AN: 151912 Hom.: 28075 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.605 AC: 91942 AN: 152030 Hom.: 28116 Cov.: 31 AF XY: 0.609 AC XY: 45290 AN XY: 74330

African (AFR) AF: 0.574 AC: 23774 AN: 41450

American (AMR) AF: 0.730 AC: 11158 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3468

East Asian (EAS) AF: 0.754 AC: 3895 AN: 5166

South Asian (SAS) AF: 0.666 AC: 3215 AN: 4824

European-Finnish (FIN) AF: 0.625 AC: 6594 AN: 10550

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39084 AN: 67966

Other (OTH) AF: 0.641 AC: 1355 AN: 2114

Alfa AF: 0.441 Hom.: 1135

Bravo AF: 0.612

Asia WGS AF: 0.700 AC: 2436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.50
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: rs601079; hg19: chr15-78869579;