rs13313479

Variant names:

• chr15-57879513-G-A
• rs13313479

Your query was ambiguous. Multiple possible variants found:

• chr15-57879513-G-A
• chr15-57879513-G-C
• chr15-57879513-G-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 0.397 in 151,820 control chromosomes in the GnomAD database, including 12,514 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 0.40 (12514 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 0 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 (SAS) allele frequency at 95% confidence interval = 0.454 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: 0.397 AC: 60258 AN: 151702 Hom.: 12506 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.397 AC: 60281 AN: 151820 Hom.: 12514 Cov.: 32 AF XY: 0.392 AC XY: 29104 AN XY: 74160

African (AFR) AF: 0.281 AC: 11625 AN: 41430

American (AMR) AF: 0.457 AC: 6979 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1513 AN: 3466

East Asian (EAS) AF: 0.367 AC: 1894 AN: 5164

South Asian (SAS) AF: 0.470 AC: 2262 AN: 4816

European-Finnish (FIN) AF: 0.338 AC: 3539 AN: 10478

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31066 AN: 67900

Other (OTH) AF: 0.431 AC: 905 AN: 2102

Alfa AF: 0.424 Hom.: 3453

Bravo AF: 0.397

Asia WGS AF: 0.442 AC: 1523 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.49
DANN	Benign	0.46
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs13313479; hg19: chr15-58171711;