rs564585

chr15-78593885-A-G

Variant summary

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

The NM_000745.4(CHRNA5):c.*632A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,874 control chromosomes in the GnomAD database, including 13,814 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 0.40 (13814 hom., cov: 31)
  • Exomes 𝑓: 0.19 (0 hom.)
• Consequence: CHRNA5 NM_000745.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

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]

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHRNA5	NM_000745.4	c.*632A>G		3_prime_UTR_variant	6/6	ENST00000299565.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHRNA5	ENST00000299565.9	c.*632A>G		3_prime_UTR_variant	6/6	1	NM_000745.4	P1
CHRNA3	ENST00000348639.7	c.1390-694T>C		intron_variant		1
CHRNA3	ENST00000559002.5	n.194-694T>C		intron_variant, non_coding_transcript_variant		1
CHRNA3	ENST00000559658.5	c.*162+29T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60490 AN: 151724 Hom.: 13782 Cov.: 31

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.387

GnomAD4 exome AF: 0.188 AC: 6 AN: 32 Hom.: 0 Cov.: 0 AF XY: 0.208 AC XY: 5 AN XY: 24

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.399 AC: 60574 AN: 151842 Hom.: 13814 Cov.: 31 AF XY: 0.405 AC XY: 30058 AN XY: 74198

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.393

Alfa AF: 0.338 Hom.: 1172

Bravo AF: 0.422

Asia WGS AF: 0.624 AC: 2169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.2
Dann	Benign	0.31

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: rs564585; hg19: chr15-78886227;