chr6-159963371-A-G

Position:

• chr6-159963371-A-G

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 0.243 in 152,104 control chromosomes in the GnomAD database, including 5,338 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 0.24 (5338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36865 AN: 151986 Hom.: 5308 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.243 AC: 36942 AN: 152104 Hom.: 5338 Cov.: 32 AF XY: 0.252 AC XY: 18721 AN XY: 74344

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.221

Alfa AF: 0.164 Hom.: 3246

Bravo AF: 0.249

Asia WGS AF: 0.318 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6934383; hg19: chr6-160384403;