15-74732991-C-T

Variant names:

• chr15-74732991-C-T
• rs17861115

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 0.0712 in 152,178 control chromosomes in the GnomAD database, including 905 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 0.071 (905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0712 AC: 10821 AN: 152060 Hom.: 898 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.0965

Gnomad FIN AF: 0.0599

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0356

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.0712 AC: 10842 AN: 152178 Hom.: 905 Cov.: 32 AF XY: 0.0765 AC XY: 5690 AN XY: 74382

African (AFR) AF: 0.0436 AC: 1809 AN: 41526

American (AMR) AF: 0.256 AC: 3903 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1270 AN: 5182

South Asian (SAS) AF: 0.0972 AC: 468 AN: 4814

European-Finnish (FIN) AF: 0.0599 AC: 635 AN: 10604

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0356 AC: 2418 AN: 67998

Other (OTH) AF: 0.0796 AC: 168 AN: 2110

Alfa AF: 0.0449 Hom.: 69

Bravo AF: 0.0859

Asia WGS AF: 0.164 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.39
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17861115; hg19: chr15-75025332;