15-63500287-A-C

Variant names:

• chr15-63500287-A-C
• rs17184382

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 0.382 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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.393 AC: 16238 AN: 41328

American (AMR) AF: 0.384 AC: 5846 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1431 AN: 3466

East Asian (EAS) AF: 0.0615 AC: 318 AN: 5174

South Asian (SAS) AF: 0.302 AC: 1454 AN: 4818

European-Finnish (FIN) AF: 0.313 AC: 3274 AN: 10470

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28031 AN: 67852

Other (OTH) AF: 0.382 AC: 804 AN: 2102

Alfa AF: 0.400 Hom.: 41660

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
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs17184382; hg19: chr15-63792486;