rs9532089

Variant names:

• chr13-37610673-G-A
• rs9532089

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 0.396 in 151,918 control chromosomes in the GnomAD database, including 12,557 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 0.40 (12557 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 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: 0.397 AC: 60189 AN: 151798 Hom.: 12552 Cov.: 33

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.396 AC: 60223 AN: 151918 Hom.: 12557 Cov.: 33 AF XY: 0.399 AC XY: 29614 AN XY: 74262

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.414

Alfa AF: 0.443 Hom.: 16359

Bravo AF: 0.382

Asia WGS AF: 0.287 AC: 1001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9532089; hg19: chr13-38184810;