6-32713854-C-T

Position:

• chr6-32713854-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.717

Alfa AF: 0.656 Hom.: 49171

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275596; hg19: chr6-32681631;