rs17303101

Variant names:

• chr9-116419515-G-A
• rs17303101

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 0.265 in 152,086 control chromosomes in the GnomAD database, including 5,492 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 0.26 (5492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 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: 0.265 AC: 40273 AN: 151968 Hom.: 5492 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.265 AC: 40289 AN: 152086 Hom.: 5492 Cov.: 32 AF XY: 0.261 AC XY: 19409 AN XY: 74358

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.284

Alfa AF: 0.284 Hom.: 7009

Bravo AF: 0.261

Asia WGS AF: 0.150 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.16
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17303101; hg19: chr9-119181794; COSMIC: COSV62538672;