15-32702642-C-T

Variant names:

• chr15-32702642-C-T
• rs9888701

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 0.24 in 152,116 control chromosomes in the GnomAD database, including 4,872 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 0.24 (4872 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 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: 0.240 AC: 36427 AN: 151998 Hom.: 4870 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.240 AC: 36440 AN: 152116 Hom.: 4872 Cov.: 33 AF XY: 0.239 AC XY: 17784 AN XY: 74346

African (AFR) AF: 0.129 AC: 5344 AN: 41510

American (AMR) AF: 0.294 AC: 4487 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3468

East Asian (EAS) AF: 0.104 AC: 537 AN: 5178

South Asian (SAS) AF: 0.260 AC: 1252 AN: 4818

European-Finnish (FIN) AF: 0.283 AC: 2995 AN: 10566

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19665 AN: 67972

Other (OTH) AF: 0.251 AC: 530 AN: 2112

Alfa AF: 0.270 Hom.: 7565

Bravo AF: 0.236

Asia WGS AF: 0.196 AC: 681 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.74
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs9888701; hg19: chr15-32994843;