rs9550642

Variant names:

• chr13-20375953-G-A
• rs9550642

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 0.0909 in 152,168 control chromosomes in the GnomAD database, including 920 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 0.091 (920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

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 = 0.277 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: 0.0909 AC: 13827 AN: 152050 Hom.: 919 Cov.: 32

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0909 AC: 13829 AN: 152168 Hom.: 920 Cov.: 32 AF XY: 0.0932 AC XY: 6936 AN XY: 74398

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.0895

Gnomad4 NFE AF: 0.0975

Gnomad4 OTH AF: 0.105

Alfa AF: 0.100 Hom.: 562

Bravo AF: 0.0921

Asia WGS AF: 0.218 AC: 758 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	0.53
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9550642; hg19: chr13-20950092;