rs17791513

chr9-79290675-A-G

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 0.0637 in 152,300 control chromosomes in the GnomAD database, including 385 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 0.064 (385 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.126 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: 0.0636 AC: 9684 AN: 152182 Hom.: 379 Cov.: 33

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.0516

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0702

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

GnomAD4 genome AF: 0.0637 AC: 9701 AN: 152300 Hom.: 385 Cov.: 33 AF XY: 0.0679 AC XY: 5057 AN XY: 74464

Gnomad4 AFR AF: 0.0334

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.0515

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.0597

Gnomad4 OTH AF: 0.0690

Alfa AF: 0.0619 Hom.: 308

Bravo AF: 0.0616

Asia WGS AF: 0.103 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	10
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17791513; hg19: chr9-81905590;