rs17184382

Positions:

• chr15-63500287-A-C
• chr15-63500287-A-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 0.382 in 151,652 control chromosomes in the GnomAD database, including 11,427 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 0.38 (11427 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57854 AN: 151534 Hom.: 11414 Cov.: 30

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.382 AC: 57917 AN: 151652 Hom.: 11427 Cov.: 30 AF XY: 0.377 AC XY: 27949 AN XY: 74116

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.0615

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.382

Alfa AF: 0.400 Hom.: 25317

Bravo AF: 0.385

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17184382; hg19: chr15-63792486;