rs9558551

Positions:

• chr13-105432673-T-G

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 0.702 in 152,028 control chromosomes in the GnomAD database, including 37,627 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 0.70 (37627 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 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: 0.702 AC: 106689 AN: 151910 Hom.: 37596 Cov.: 33

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.702 AC: 106786 AN: 152028 Hom.: 37627 Cov.: 33 AF XY: 0.701 AC XY: 52058 AN XY: 74294

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.709

Alfa AF: 0.696 Hom.: 68759

Bravo AF: 0.712

Asia WGS AF: 0.730 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9558551; hg19: chr13-106085022;