rs17352842

Positions:

• chr15-48402014-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;