chr15-78652376-G-A

Position:

• chr15-78652376-G-A

Variant summary

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

The ENST00000559849.5(CHRNB4):​c.-16+202C>T variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,264 control chromosomes in the GnomAD database, including 7,464 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 0.28 (7464 hom., cov: 33)
• Consequence: CHRNB4 ENST00000559849.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

Genes affected

CHRNB4 (HGNC:1964): (cholinergic receptor nicotinic beta 4 subunit) This gene is found within a conserved gene cluster and encodes one of the beta subunits of the nicotinic acetylcholine receptor (nAChRs) superfamily which form ligand-gated ion channels with a central pore that forms a cation channel. Neuronal nAChRs are pentameric structures that can be either homomeric or heteromeric, with heteromeric structures containing both alpha and beta subunits. Each subunit contains an extracellular amino terminus and four transmembrane domains. Nicotine is one of the agonists that binds to the receptor. Variants in this gene have been associated with nicotine dependence and lung cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHRNB4	XM_011521186.3	c.-16+202C>T		intron_variant			XP_011519488.1
CHRNB4	XM_011521187.3	c.-15-2937C>T		intron_variant			XP_011519489.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHRNB4	ENST00000559849.5	c.-16+202C>T		intron_variant, NMD_transcript_variant		1		ENSP00000457404
CHRNB4	ENST00000560511.5	n.349-2937C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.276 AC: 42058 AN: 152146 Hom.: 7461 Cov.: 33

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.276 AC: 42061 AN: 152264 Hom.: 7464 Cov.: 33 AF XY: 0.272 AC XY: 20233 AN XY: 74440

Gnomad4 AFR AF: 0.0797

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.0252

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.304

Alfa AF: 0.329 Hom.: 1157

Bravo AF: 0.261

Asia WGS AF: 0.116 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.1
DANN	Benign	0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11634351; hg19: chr15-78944718;