rs9550855

Variant names:

• chr13-22662653-G-A
• rs9550855

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 0.258 in 151,992 control chromosomes in the GnomAD database, including 5,357 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 0.26 (5357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 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: 0.258 AC: 39195 AN: 151876 Hom.: 5357 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.258 AC: 39194 AN: 151992 Hom.: 5357 Cov.: 32 AF XY: 0.261 AC XY: 19391 AN XY: 74300

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.272

Alfa AF: 0.253 Hom.: 953

Bravo AF: 0.241

Asia WGS AF: 0.269 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9550855; hg19: chr13-23236792;