rs12585963

Variant names:

• chr13-59379332-G-A
• rs12585963

Your query was ambiguous. Multiple possible variants found:

• chr13-59379332-G-A
• chr13-59379332-G-C

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 0.326 in 151,940 control chromosomes in the GnomAD database, including 8,311 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 0.33 (8311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.326 AC: 49483 AN: 151822 Hom.: 8302 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.326 AC: 49525 AN: 151940 Hom.: 8311 Cov.: 32 AF XY: 0.322 AC XY: 23896 AN XY: 74280

African (AFR) AF: 0.392 AC: 16229 AN: 41414

American (AMR) AF: 0.302 AC: 4608 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1773 AN: 5146

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4816

European-Finnish (FIN) AF: 0.254 AC: 2685 AN: 10582

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20672 AN: 67940

Other (OTH) AF: 0.333 AC: 703 AN: 2108

Alfa AF: 0.681 Hom.: 10604

Bravo AF: 0.337

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.26
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs12585963; hg19: chr13-59953466;