rs6934383

Variant names:

• chr6-159963371-A-G
• rs6934383

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.363 AC: 15042 AN: 41462

American (AMR) AF: 0.271 AC: 4138 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3472

East Asian (EAS) AF: 0.450 AC: 2328 AN: 5170

South Asian (SAS) AF: 0.181 AC: 873 AN: 4826

European-Finnish (FIN) AF: 0.296 AC: 3134 AN: 10580

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10441 AN: 67990

Other (OTH) AF: 0.221 AC: 467 AN: 2112

Alfa AF: 0.177 Hom.: 5632

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs6934383; hg19: chr6-160384403;