rs17701704

Variant names:

• chr9-25396791-A-G
• rs17701704

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 0.126 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0563 AC: 2335 AN: 41498

American (AMR) AF: 0.0951 AC: 1451 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1200 AN: 5124

South Asian (SAS) AF: 0.204 AC: 980 AN: 4814

European-Finnish (FIN) AF: 0.180 AC: 1906 AN: 10572

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10437 AN: 67938

Other (OTH) AF: 0.126 AC: 266 AN: 2116

Alfa AF: 0.139 Hom.: 5129

Bravo AF: 0.115

Asia WGS AF: 0.172 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.67
PhyloP100		0.52

Splicing

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

Other links and lift over

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