13-105861607-A-C

Variant names:

• chr13-105861607-A-C
• rs2476761

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 0.747 in 152,096 control chromosomes in the GnomAD database, including 42,596 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 0.75 (42596 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.747 AC: 113583 AN: 151978 Hom.: 42554 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.747 AC: 113677 AN: 152096 Hom.: 42596 Cov.: 32 AF XY: 0.750 AC XY: 55778 AN XY: 74356

African (AFR) AF: 0.724 AC: 30031 AN: 41478

American (AMR) AF: 0.765 AC: 11694 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2853 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4796 AN: 5176

South Asian (SAS) AF: 0.771 AC: 3720 AN: 4822

European-Finnish (FIN) AF: 0.735 AC: 7769 AN: 10572

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50265 AN: 67978

Other (OTH) AF: 0.777 AC: 1643 AN: 2114

Alfa AF: 0.710 Hom.: 4447

Bravo AF: 0.751

Asia WGS AF: 0.831 AC: 2888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.95
DANN	Benign	0.54
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2476761; hg19: chr13-106513956;