6-31094890-T-C

Variant names:

• chr6-31094890-T-C
• rs2517448

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 0.658 in 151,396 control chromosomes in the GnomAD database, including 33,047 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 (33047 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 38 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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: 0.658 AC: 99507 AN: 151278 Hom.: 33015 Cov.: 27

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.658 AC: 99580 AN: 151396 Hom.: 33047 Cov.: 27 AF XY: 0.656 AC XY: 48522 AN XY: 73942

African (AFR) AF: 0.727 AC: 29997 AN: 41234

American (AMR) AF: 0.609 AC: 9271 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2931 AN: 3466

East Asian (EAS) AF: 0.641 AC: 3266 AN: 5096

South Asian (SAS) AF: 0.723 AC: 3434 AN: 4748

European-Finnish (FIN) AF: 0.608 AC: 6390 AN: 10506

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41938 AN: 67814

Other (OTH) AF: 0.692 AC: 1455 AN: 2104

Alfa AF: 0.635 Hom.: 109899

Bravo AF: 0.660

Asia WGS AF: 0.668 AC: 2327 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	0.89
DANN	Benign	0.68
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs2517448; hg19: chr6-31062667;