rs17702901

Variant names:

• chr15-92387181-G-A
• rs17702901

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 0.056 in 152,246 control chromosomes in the GnomAD database, including 436 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 0.056 (436 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.78

ACMG classification

Verdict is Benign. Variant got -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 = 0.152 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: 0.0559 AC: 8504 AN: 152128 Hom.: 431 Cov.: 33

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0560 AC: 8528 AN: 152246 Hom.: 436 Cov.: 33 AF XY: 0.0596 AC XY: 4436 AN XY: 74442

Gnomad4 AFR AF: 0.0433

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0341

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0460 Hom.: 48

Bravo AF: 0.0649

Asia WGS AF: 0.150 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0070
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17702901; hg19: chr15-92930411;