15-74733647-C-T

Variant names:

• chr15-74733647-C-T
• rs4886605

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 0.31 in 151,924 control chromosomes in the GnomAD database, including 9,888 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 0.31 (9888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 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: 0.310 AC: 47008 AN: 151806 Hom.: 9845 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.310 AC: 47127 AN: 151924 Hom.: 9888 Cov.: 32 AF XY: 0.315 AC XY: 23414 AN XY: 74274

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.306

Alfa AF: 0.199 Hom.: 4046

Bravo AF: 0.338

Asia WGS AF: 0.529 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4886605; hg19: chr15-75025988;