rs13379705

Variant names:

• chr15-48352611-T-C
• rs13379705

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 0.178 in 152,182 control chromosomes in the GnomAD database, including 2,652 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 0.18 (2652 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 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: 0.178 AC: 27096 AN: 152064 Hom.: 2647 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.178 AC: 27132 AN: 152182 Hom.: 2652 Cov.: 32 AF XY: 0.179 AC XY: 13292 AN XY: 74392

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.199

Alfa AF: 0.165 Hom.: 276

Bravo AF: 0.182

Asia WGS AF: 0.319 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13379705; hg19: chr15-48644808;