rs732589

Variant names:

• chr17-45393394-C-T
• rs732589

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 0.359 in 152,054 control chromosomes in the GnomAD database, including 10,434 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 0.36 (10434 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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: 0.359 AC: 54532 AN: 151936 Hom.: 10422 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.359 AC: 54583 AN: 152054 Hom.: 10434 Cov.: 33 AF XY: 0.360 AC XY: 26757 AN XY: 74310

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.377

Alfa AF: 0.311 Hom.: 2360

Bravo AF: 0.368

Asia WGS AF: 0.412 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs732589; hg19: chr17-43470760;