rs9559892

chr13-88716410-C-A

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 0.115 in 151,904 control chromosomes in the GnomAD database, including 1,628 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 0.12 (1628 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17481 AN: 151786 Hom.: 1619 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.115 AC: 17513 AN: 151904 Hom.: 1628 Cov.: 32 AF XY: 0.119 AC XY: 8830 AN XY: 74254

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0413

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0827 Hom.: 108

Bravo AF: 0.118

Asia WGS AF: 0.177 AC: 610 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.15
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9559892; hg19: chr13-89368664;