rs16891620

Variant names:

• chr8-42770520-C-A
• rs16891620
• ENST00000533810.5:c.-158-5316G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-42770520-C-A
• chr8-42770520-C-T

Variant summary

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

The ENST00000533810.5(CHRNA6):​c.-158-5316G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 150,380 control chromosomes in the GnomAD database, including 1,694 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 0.14 (1694 hom., cov: 30)
• Consequence: CHRNA6 ENST00000533810.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 8 publications found

Genes affected

CHRNA6 (HGNC:15963): (cholinergic receptor nicotinic alpha 6 subunit) This gene encodes an alpha subunit of neuronal nicotinic acetylcholine receptors. These receptors consist of five subunits and function as ion channels involved in neurotransmission. The encoded protein is a subunit of neuronal nicotinic acetylcholine receptors that mediate dopaminergic neurotransmission and are activated by acetylcholine and exogenous nicotine. Alternatively spliced transcript variants have been observed for this gene. Single nucleotide polymorphisms in this gene have been associated with both nicotine and alcohol dependence. [provided by RefSeq, Dec 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533810.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHRNA6	ENST00000533810.5	TSL:4	c.-158-5316G>T		intron	N/A	ENSP00000434659.1

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20433 AN: 150314 Hom.: 1691 Cov.: 30

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00156

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.136 AC: 20473 AN: 150380 Hom.: 1694 Cov.: 30 AF XY: 0.128 AC XY: 9398 AN XY: 73268

African (AFR) AF: 0.213 AC: 8680 AN: 40704

American (AMR) AF: 0.112 AC: 1691 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3470

East Asian (EAS) AF: 0.00156 AC: 8 AN: 5116

South Asian (SAS) AF: 0.0372 AC: 177 AN: 4756

European-Finnish (FIN) AF: 0.0548 AC: 556 AN: 10144

Middle Eastern (MID) AF: 0.0944 AC: 27 AN: 286

European-Non Finnish (NFE) AF: 0.127 AC: 8605 AN: 67834

Other (OTH) AF: 0.138 AC: 286 AN: 2072

Alfa AF: 0.128 Hom.: 4493

Bravo AF: 0.146

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.72
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs16891620; hg19: chr8-42625663;