rs13289810

chr9-12396731-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 0.282 in 152,100 control chromosomes in the GnomAD database, including 6,465 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 0.28 (6465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 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: 0.282 AC: 42922 AN: 151982 Hom.: 6462 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.282 AC: 42953 AN: 152100 Hom.: 6465 Cov.: 32 AF XY: 0.275 AC XY: 20413 AN XY: 74354

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.306

Alfa AF: 0.291 Hom.: 1117

Bravo AF: 0.280

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.3
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13289810; hg19: chr9-12396731;