rs17701704

Variant names:

• chr9-25396791-A-G
• rs17701704

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;