9-26694890-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 0.198 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;