rs2785946

Variant names:

• chr13-54355063-A-G
• rs2785946

Your query was ambiguous. Multiple possible variants found:

• chr13-54355063-A-G
• chr13-54355063-A-T

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 0.721 in 152,054 control chromosomes in the GnomAD database, including 40,177 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 0.72 (40177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 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: 0.720 AC: 109451 AN: 151936 Hom.: 40117 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.721 AC: 109576 AN: 152054 Hom.: 40177 Cov.: 32 AF XY: 0.718 AC XY: 53374 AN XY: 74308

African (AFR) AF: 0.845 AC: 35085 AN: 41512

American (AMR) AF: 0.757 AC: 11558 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2731 AN: 3468

East Asian (EAS) AF: 0.699 AC: 3606 AN: 5156

South Asian (SAS) AF: 0.559 AC: 2697 AN: 4824

European-Finnish (FIN) AF: 0.652 AC: 6890 AN: 10568

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44885 AN: 67954

Other (OTH) AF: 0.734 AC: 1547 AN: 2108

Alfa AF: 0.698 Hom.: 45845

Bravo AF: 0.741

Asia WGS AF: 0.621 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.32
DANN	Benign	0.66
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2785946; hg19: chr13-54929198; COSMIC: COSV69350709;