rs17861118

chr15-74733808-G-A

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 0.0598 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.0512

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.000776

Gnomad4 SAS AF: 0.0492

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0850

Gnomad4 OTH AF: 0.0731

Alfa AF: 0.0767 Hom.: 110

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17861118; hg19: chr15-75026149;