6-32699503-A-G

Variant names:

• chr6-32699503-A-G
• rs2647040

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 0.645 in 151,960 control chromosomes in the GnomAD database, including 32,058 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 (32058 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• 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: 0.645 AC: 97965 AN: 151842 Hom.: 32036 Cov.: 31

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.655

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: 0.645 AC: 98039 AN: 151960 Hom.: 32058 Cov.: 31 AF XY: 0.650 AC XY: 48242 AN XY: 74254

African (AFR) AF: 0.635 AC: 26300 AN: 41432

American (AMR) AF: 0.740 AC: 11311 AN: 15276

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

East Asian (EAS) AF: 0.818 AC: 4241 AN: 5184

South Asian (SAS) AF: 0.680 AC: 3279 AN: 4820

European-Finnish (FIN) AF: 0.655 AC: 6884 AN: 10502

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

European-Non Finnish (NFE) AF: 0.603 AC: 40981 AN: 67962

Other (OTH) AF: 0.689 AC: 1452 AN: 2108

Alfa AF: 0.622 Hom.: 4338

Bravo AF: 0.656

Asia WGS AF: 0.765 AC: 2663 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.44
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2647040; hg19: chr6-32667280;