rs9558551

Variant names:

• chr13-105432673-T-G
• rs9558551

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.698 AC: 28959 AN: 41500

American (AMR) AF: 0.759 AC: 11584 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2351 AN: 3468

East Asian (EAS) AF: 0.767 AC: 3957 AN: 5160

South Asian (SAS) AF: 0.710 AC: 3425 AN: 4824

European-Finnish (FIN) AF: 0.668 AC: 7047 AN: 10546

Middle Eastern (MID) AF: 0.766 AC: 222 AN: 290

European-Non Finnish (NFE) AF: 0.695 AC: 47220 AN: 67950

Other (OTH) AF: 0.709 AC: 1497 AN: 2110

Alfa AF: 0.698 Hom.: 89951

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs9558551; hg19: chr13-106085022;