rs6731116

Positions:

• chr2-104292045-G-C

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 0.762 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.770

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6731116; hg19: chr2-104908503;