rs17352842

Variant names:

• chr15-48402014-C-T
• rs17352842

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 0.182 in 151,938 control chromosomes in the GnomAD database, including 2,659 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 (2659 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 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: 0.182 AC: 27627 AN: 151820 Hom.: 2657 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.182 AC: 27649 AN: 151938 Hom.: 2659 Cov.: 32 AF XY: 0.178 AC XY: 13191 AN XY: 74282

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0400

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.189

Alfa AF: 0.195 Hom.: 3567

Bravo AF: 0.185

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.058
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17352842; hg19: chr15-48694211;