rs13379705

Variant names:

• chr15-48352611-T-C
• rs13379705

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 0.178 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.189 AC: 7843 AN: 41550

American (AMR) AF: 0.189 AC: 2893 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 632 AN: 3470

East Asian (EAS) AF: 0.406 AC: 2090 AN: 5154

South Asian (SAS) AF: 0.215 AC: 1036 AN: 4824

European-Finnish (FIN) AF: 0.135 AC: 1430 AN: 10602

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10652 AN: 67970

Other (OTH) AF: 0.199 AC: 419 AN: 2110

Alfa AF: 0.166 Hom.: 288

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
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs13379705; hg19: chr15-48644808;