6-32713854-C-T

Variant names:

• chr6-32713854-C-T
• rs9275596

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 0.67 in 152,052 control chromosomes in the GnomAD database, including 34,584 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 0.67 (34584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 109 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 = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101775 AN: 151934 Hom.: 34560 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.670 AC: 101849 AN: 152052 Hom.: 34584 Cov.: 32 AF XY: 0.674 AC XY: 50112 AN XY: 74316

African (AFR) AF: 0.650 AC: 26951 AN: 41438

American (AMR) AF: 0.760 AC: 11614 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2749 AN: 3470

East Asian (EAS) AF: 0.858 AC: 4454 AN: 5192

South Asian (SAS) AF: 0.765 AC: 3683 AN: 4812

European-Finnish (FIN) AF: 0.665 AC: 7021 AN: 10554

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42921 AN: 67980

Other (OTH) AF: 0.717 AC: 1516 AN: 2114

Alfa AF: 0.651 Hom.: 128450

Bravo AF: 0.679

Asia WGS AF: 0.837 AC: 2912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.62
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9275596; hg19: chr6-32681631;