9-26694890-A-G

Variant names:

• chr9-26694890-A-G
• rs13294589

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 0.198 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.198 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

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.0873

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.213

Alfa AF: 0.190 Hom.: 3947

Bravo AF: 0.205

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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