rs17303101

Variant names:

• chr9-116419515-G-A
• rs17303101

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 0.265 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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.250 AC: 10377 AN: 41470

American (AMR) AF: 0.237 AC: 3614 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1100 AN: 3472

East Asian (EAS) AF: 0.118 AC: 608 AN: 5162

South Asian (SAS) AF: 0.212 AC: 1023 AN: 4818

European-Finnish (FIN) AF: 0.262 AC: 2776 AN: 10588

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.292 AC: 19823 AN: 67982

Other (OTH) AF: 0.284 AC: 600 AN: 2114

Alfa AF: 0.278 Hom.: 12000

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
PhyloP100		-0.83

Splicing

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

Other links and lift over

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