rs9552104

Variant names:

• chr13-20201858-G-C
• rs9552104

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 0.124 in 152,136 control chromosomes in the GnomAD database, including 1,758 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 (1758 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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: 0.124 AC: 18873 AN: 152018 Hom.: 1749 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.124 AC: 18924 AN: 152136 Hom.: 1758 Cov.: 32 AF XY: 0.128 AC XY: 9489 AN XY: 74382

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.0735

Gnomad4 FIN AF: 0.0321

Gnomad4 NFE AF: 0.0641

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0960 Hom.: 127

Bravo AF: 0.144

Asia WGS AF: 0.214 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.75
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9552104; hg19: chr13-20775997;