rs9590141

Variant names:

• chr13-94951368-G-A
• rs9590141

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 0.0822 in 152,252 control chromosomes in the GnomAD database, including 587 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 0.082 (587 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 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: 0.0821 AC: 12483 AN: 152134 Hom.: 583 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0453

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0497

Gnomad FIN AF: 0.0418

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0822 AC: 12508 AN: 152252 Hom.: 587 Cov.: 32 AF XY: 0.0788 AC XY: 5868 AN XY: 74468

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0451

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0493

Gnomad4 FIN AF: 0.0418

Gnomad4 NFE AF: 0.0872

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0856 Hom.: 467

Bravo AF: 0.0829

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9590141; hg19: chr13-95603622;