6-32702531-A-G

Variant names:

• chr6-32702531-A-G
• rs2856717

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 0.646 in 151,944 control chromosomes in the GnomAD database, including 32,083 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 0.65 (32083 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 79 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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: 0.646 AC: 98010 AN: 151826 Hom.: 32061 Cov.: 31

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.646 AC: 98084 AN: 151944 Hom.: 32083 Cov.: 31 AF XY: 0.650 AC XY: 48279 AN XY: 74276

African (AFR) AF: 0.635 AC: 26308 AN: 41420

American (AMR) AF: 0.740 AC: 11313 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2682 AN: 3470

East Asian (EAS) AF: 0.818 AC: 4228 AN: 5166

South Asian (SAS) AF: 0.681 AC: 3276 AN: 4810

European-Finnish (FIN) AF: 0.656 AC: 6913 AN: 10538

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41009 AN: 67952

Other (OTH) AF: 0.689 AC: 1450 AN: 2104

Alfa AF: 0.626 Hom.: 113118

Bravo AF: 0.656

Asia WGS AF: 0.769 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.6
DANN	Benign	0.68
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs2856717; hg19: chr6-32670308;