15-78572855-A-G

Variant names:

• chr15-78572855-A-G
• rs17486195
• NM_000745.4:c.106+7030A>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.106+7030A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,076 control chromosomes in the GnomAD database, including 6,065 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 0.26 (6065 hom., cov: 32)
• Consequence: CHRNA5 NM_000745.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 21 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000745.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHRNA5	NM_000745.4	MANE Select	c.106+7030A>G		intron	N/A	NP_000736.2
	CHRNA5	NM_001395171.1		c.106+7030A>G		intron	N/A	NP_001382100.1
	CHRNA5	NM_001395172.1		c.106+7030A>G		intron	N/A	NP_001382101.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHRNA5	ENST00000299565.9	TSL:1 MANE Select	c.106+7030A>G		intron	N/A	ENSP00000299565.5	P30532
	CHRNA5	ENST00000913028.1		c.106+7030A>G		intron	N/A	ENSP00000583087.1
	CHRNA5	ENST00000559554.5	TSL:3	c.106+7030A>G		intron	N/A	ENSP00000453519.1	H0YM98

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39419 AN: 151958 Hom.: 6064 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.259 AC: 39435 AN: 152076 Hom.: 6065 Cov.: 32 AF XY: 0.256 AC XY: 19039 AN XY: 74352

African (AFR) AF: 0.124 AC: 5133 AN: 41472

American (AMR) AF: 0.234 AC: 3577 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3470

East Asian (EAS) AF: 0.0334 AC: 173 AN: 5184

South Asian (SAS) AF: 0.224 AC: 1079 AN: 4816

European-Finnish (FIN) AF: 0.328 AC: 3465 AN: 10576

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23586 AN: 67974

Other (OTH) AF: 0.292 AC: 615 AN: 2104

Alfa AF: 0.205 Hom.: 817

Bravo AF: 0.245

Asia WGS AF: 0.121 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.52
PhyloP100		-0.40
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: rs17486195; hg19: chr15-78865197;