rs13289810

Variant names:

• chr9-12396731-A-G
• rs13289810

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 0.282 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.239 AC: 9918 AN: 41510

American (AMR) AF: 0.239 AC: 3640 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1614 AN: 3462

East Asian (EAS) AF: 0.0470 AC: 243 AN: 5174

South Asian (SAS) AF: 0.245 AC: 1177 AN: 4810

European-Finnish (FIN) AF: 0.219 AC: 2319 AN: 10590

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22947 AN: 67976

Other (OTH) AF: 0.306 AC: 646 AN: 2114

Alfa AF: 0.310 Hom.: 12505

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
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs13289810; hg19: chr9-12396731;