6-32702687-G-T

Variant names:

• chr6-32702687-G-T
• rs2858305

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 151,992 control chromosomes in the GnomAD database, including 32,105 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 (32105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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: 0.646 AC: 98065 AN: 151872 Hom.: 32083 Cov.: 32

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: 0.682

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.646 AC: 98140 AN: 151992 Hom.: 32105 Cov.: 32 AF XY: 0.650 AC XY: 48316 AN XY: 74286

African (AFR) AF: 0.635 AC: 26316 AN: 41428

American (AMR) AF: 0.740 AC: 11316 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2678 AN: 3464

East Asian (EAS) AF: 0.818 AC: 4250 AN: 5194

South Asian (SAS) AF: 0.681 AC: 3280 AN: 4818

European-Finnish (FIN) AF: 0.657 AC: 6914 AN: 10516

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

European-Non Finnish (NFE) AF: 0.604 AC: 41022 AN: 67972

Other (OTH) AF: 0.690 AC: 1455 AN: 2110

Alfa AF: 0.635 Hom.: 34209

Bravo AF: 0.656

Asia WGS AF: 0.770 AC: 2680 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	2.0
DANN	Benign	0.24
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2858305; hg19: chr6-32670464;