15-74733647-C-T

Variant names:

• chr15-74733647-C-T
• rs4886605

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 0.31 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
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.536 AC: 22196 AN: 41374

American (AMR) AF: 0.419 AC: 6393 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3468

East Asian (EAS) AF: 0.599 AC: 3099 AN: 5174

South Asian (SAS) AF: 0.376 AC: 1807 AN: 4812

European-Finnish (FIN) AF: 0.146 AC: 1549 AN: 10578

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10270 AN: 67946

Other (OTH) AF: 0.306 AC: 646 AN: 2114

Alfa AF: 0.218 Hom.: 7883

Bravo AF: 0.338

Asia WGS AF: 0.529 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.12
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs4886605; hg19: chr15-75025988;