rs6495314

Positions:

• chr15-78668187-A-C

Variant summary

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

The variant allele was found at a frequency of 0.347 in 152,100 control chromosomes in the GnomAD database, including 9,416 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 0.35 (9416 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78668187A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHRNB4	ENST00000560511.5	n.229-12524T>G		intron_variant		3
ENSG00000290426	ENST00000569846.1	n.366+6653A>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52699 AN: 151978 Hom.: 9415 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.347 AC: 52718 AN: 152100 Hom.: 9416 Cov.: 33 AF XY: 0.342 AC XY: 25438 AN XY: 74352

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.349

Alfa AF: 0.395 Hom.: 24495

Bravo AF: 0.341

Asia WGS AF: 0.274 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6495314; hg19: chr15-78960529;