rs17701704

chr9-25396791-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 0.126 in 151,996 control chromosomes in the GnomAD database, including 1,439 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 0.13 (1439 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516

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 (EAS) allele frequency at 95% confidence interval = 0.223 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: 0.126 AC: 19204 AN: 151880 Hom.: 1441 Cov.: 32

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.126 AC: 19198 AN: 151996 Hom.: 1439 Cov.: 32 AF XY: 0.129 AC XY: 9591 AN XY: 74296

Gnomad4 AFR AF: 0.0563

Gnomad4 AMR AF: 0.0951

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.126

Alfa AF: 0.145 Hom.: 3437

Bravo AF: 0.115

Asia WGS AF: 0.172 AC: 598 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	5.4
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17701704; hg19: chr9-25396789; COSMIC: COSV60344852;