chr9-26694890-A-G

Variant names:

• chr9-26694890-A-G
• rs13294589

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 0.198 in 152,016 control chromosomes in the GnomAD database, including 3,038 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 0.20 (3038 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.846
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 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: 0.198 AC: 30080 AN: 151898 Hom.: 3032 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.198 AC: 30107 AN: 152016 Hom.: 3038 Cov.: 31 AF XY: 0.197 AC XY: 14649 AN XY: 74336

African (AFR) AF: 0.191 AC: 7921 AN: 41470

American (AMR) AF: 0.265 AC: 4049 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3466

East Asian (EAS) AF: 0.0873 AC: 451 AN: 5168

South Asian (SAS) AF: 0.153 AC: 735 AN: 4800

European-Finnish (FIN) AF: 0.204 AC: 2166 AN: 10592

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13533 AN: 67950

Other (OTH) AF: 0.213 AC: 450 AN: 2108

Alfa AF: 0.194 Hom.: 10270

Bravo AF: 0.205

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.71
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs13294589; hg19: chr9-26694888; COSMIC: COSV50193300;