6-132424824-G-A

Variant names:

• chr6-132424824-G-A
• rs6937815

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 0.0649 in 152,070 control chromosomes in the GnomAD database, including 692 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 0.065 (692 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0649 AC: 9868 AN: 151952 Hom.: 695 Cov.: 32

Gnomad AFR AF: 0.0400

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.0328

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0695

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

GnomAD4 genome AF: 0.0649 AC: 9872 AN: 152070 Hom.: 692 Cov.: 32 AF XY: 0.0677 AC XY: 5029 AN XY: 74336

African (AFR) AF: 0.0400 AC: 1658 AN: 41486

American (AMR) AF: 0.136 AC: 2075 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3470

East Asian (EAS) AF: 0.393 AC: 2017 AN: 5138

South Asian (SAS) AF: 0.0326 AC: 157 AN: 4818

European-Finnish (FIN) AF: 0.0287 AC: 304 AN: 10586

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0477 AC: 3245 AN: 67990

Other (OTH) AF: 0.0693 AC: 146 AN: 2108

Alfa AF: 0.0203 Hom.: 23

Bravo AF: 0.0750

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.40
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs6937815; hg19: chr6-132745963;