rs13362504

Variant names:

• chr5-56683302-A-C
• rs13362504

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 0.285 in 151,962 control chromosomes in the GnomAD database, including 6,701 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 0.29 (6701 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 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: 0.285 AC: 43337 AN: 151844 Hom.: 6691 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.285 AC: 43375 AN: 151962 Hom.: 6701 Cov.: 32 AF XY: 0.287 AC XY: 21355 AN XY: 74288

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.291

Alfa AF: 0.249 Hom.: 2318

Bravo AF: 0.305

Asia WGS AF: 0.224 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13362504; hg19: chr5-55979129;