rs17861140

Variant names:

• chr15-74742581-G-A
• rs17861140

Your query was ambiguous. Multiple possible variants found:

• chr15-74742581-G-A
• chr15-74742581-G-C
• chr15-74742581-G-T

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 0.127 in 152,094 control chromosomes in the GnomAD database, including 2,566 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 0.13 (2566 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 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: 0.127 AC: 19305 AN: 151976 Hom.: 2548 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.0488

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0131

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.127 AC: 19374 AN: 152094 Hom.: 2566 Cov.: 31 AF XY: 0.131 AC XY: 9746 AN XY: 74382

African (AFR) AF: 0.278 AC: 11528 AN: 41406

American (AMR) AF: 0.273 AC: 4172 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1371 AN: 5166

South Asian (SAS) AF: 0.0821 AC: 396 AN: 4826

European-Finnish (FIN) AF: 0.0488 AC: 518 AN: 10612

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0131 AC: 892 AN: 68018

Other (OTH) AF: 0.114 AC: 241 AN: 2112

Alfa AF: 0.0544 Hom.: 393

Bravo AF: 0.154

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.59
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs17861140; hg19: chr15-75034922;