rs9532089

Variant names:

• chr13-37610673-G-A
• rs9532089
• ENST00000744989.1:n.48+13636G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000744989.1(ENSG00000297050):​n.48+13636G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359
• Publications: 2 publications found

Genes affected

ENSG00000297050 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000297050	ENST00000744989.1	n.48+13636G>A		intron_variant	Intron 1 of 4
ENSG00000297050	ENST00000744990.1	n.70+13636G>A		intron_variant	Intron 1 of 5

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

African (AFR) AF: 0.302 AC: 12487 AN: 41416

American (AMR) AF: 0.413 AC: 6302 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1223 AN: 3470

East Asian (EAS) AF: 0.153 AC: 789 AN: 5148

South Asian (SAS) AF: 0.365 AC: 1757 AN: 4816

European-Finnish (FIN) AF: 0.504 AC: 5313 AN: 10542

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30791 AN: 67956

Other (OTH) AF: 0.414 AC: 871 AN: 2106

Alfa AF: 0.435 Hom.: 45406

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs9532089; hg19: chr13-38184810;