6-31039813-C-T

Variant names:

• chr6-31039813-C-T
• rs2517552

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 0.656 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
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.719 AC: 29760 AN: 41408

American (AMR) AF: 0.621 AC: 9476 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2875 AN: 3470

East Asian (EAS) AF: 0.492 AC: 2539 AN: 5158

South Asian (SAS) AF: 0.662 AC: 3189 AN: 4814

European-Finnish (FIN) AF: 0.619 AC: 6514 AN: 10520

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42870 AN: 67950

Other (OTH) AF: 0.696 AC: 1458 AN: 2096

Alfa AF: 0.643 Hom.: 124207

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
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2517552; hg19: chr6-31007590;