chr6-31039813-C-T

Position:

• chr6-31039813-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 0.656 in 151,876 control chromosomes in the GnomAD database, including 32,919 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 0.66 (32919 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 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: 0.656 AC: 99491 AN: 151758 Hom.: 32887 Cov.: 30

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.656 AC: 99568 AN: 151876 Hom.: 32919 Cov.: 30 AF XY: 0.653 AC XY: 48434 AN XY: 74204

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.696

Alfa AF: 0.646 Hom.: 46982

Bravo AF: 0.661

Asia WGS AF: 0.642 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.64
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517552; hg19: chr6-31007590;