rs13313479

chr15-57879513-G-Achr15-57879513-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 0.397 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.431

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13313479; hg19: chr15-58171711;