6-32692598-A-G

Variant names:

• chr6-32692598-A-G
• rs2858324

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 0.639 in 151,530 control chromosomes in the GnomAD database, including 31,332 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 0.64 (31332 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96762 AN: 151412 Hom.: 31310 Cov.: 30

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.639 AC: 96835 AN: 151530 Hom.: 31332 Cov.: 30 AF XY: 0.643 AC XY: 47615 AN XY: 74004

African (AFR) AF: 0.624 AC: 25772 AN: 41278

American (AMR) AF: 0.728 AC: 11080 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2646 AN: 3460

East Asian (EAS) AF: 0.818 AC: 4203 AN: 5140

South Asian (SAS) AF: 0.679 AC: 3264 AN: 4806

European-Finnish (FIN) AF: 0.653 AC: 6816 AN: 10434

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.600 AC: 40715 AN: 67876

Other (OTH) AF: 0.681 AC: 1434 AN: 2106

Alfa AF: 0.619 Hom.: 66000

Bravo AF: 0.650

Asia WGS AF: 0.766 AC: 2661 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.83
DANN	Benign	0.28
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs2858324; hg19: chr6-32660375;