rs6731116

Variant names:

• chr2-104292045-G-C
• rs6731116

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 0.762 in 152,088 control chromosomes in the GnomAD database, including 44,635 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 0.76 (44635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.811 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: 0.762 AC: 115762 AN: 151970 Hom.: 44599 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.762 AC: 115845 AN: 152088 Hom.: 44635 Cov.: 32 AF XY: 0.753 AC XY: 56000 AN XY: 74348

African (AFR) AF: 0.730 AC: 30270 AN: 41472

American (AMR) AF: 0.759 AC: 11606 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2832 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2086 AN: 5158

South Asian (SAS) AF: 0.679 AC: 3276 AN: 4828

European-Finnish (FIN) AF: 0.711 AC: 7505 AN: 10562

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55562 AN: 67992

Other (OTH) AF: 0.770 AC: 1628 AN: 2114

Alfa AF: 0.798 Hom.: 6058

Bravo AF: 0.764

Asia WGS AF: 0.551 AC: 1913 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.56
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs6731116; hg19: chr2-104908503;