rs17861118

Variant names:

• chr15-74733808-G-A
• rs17861118

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 0.0598 in 151,844 control chromosomes in the GnomAD database, including 368 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 0.060 (368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.0831 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: 0.0598 AC: 9080 AN: 151724 Hom.: 369 Cov.: 32

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0514

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000774

Gnomad SAS AF: 0.0490

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.0739

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

GnomAD4 genome AF: 0.0598 AC: 9076 AN: 151844 Hom.: 368 Cov.: 32 AF XY: 0.0589 AC XY: 4372 AN XY: 74174

African (AFR) AF: 0.0145 AC: 600 AN: 41388

American (AMR) AF: 0.0512 AC: 781 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 395 AN: 3464

East Asian (EAS) AF: 0.000776 AC: 4 AN: 5156

South Asian (SAS) AF: 0.0492 AC: 236 AN: 4794

European-Finnish (FIN) AF: 0.102 AC: 1074 AN: 10544

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0850 AC: 5772 AN: 67936

Other (OTH) AF: 0.0731 AC: 154 AN: 2106

Alfa AF: 0.0646 Hom.: 190

Bravo AF: 0.0551

Asia WGS AF: 0.0150 AC: 54 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	3.5
DANN	Benign	0.34
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs17861118; hg19: chr15-75026149;