6-31382927-C-T

Position:

• chr6-31382927-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 0.749 in 152,104 control chromosomes in the GnomAD database, including 43,077 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 0.75 (43077 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113840 AN: 151984 Hom.: 43032 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.749 AC: 113936 AN: 152104 Hom.: 43077 Cov.: 31 AF XY: 0.756 AC XY: 56248 AN XY: 74372

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.739

Alfa AF: 0.752 Hom.: 49503

Bravo AF: 0.735

Asia WGS AF: 0.866 AC: 3013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1521; hg19: chr6-31350704;