rs920833

chrX-15087479-T-C

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 0.103 in 111,316 control chromosomes in the GnomAD database, including 840 homozygotes. There are 3,193 hemizygotes in GnomAD. 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 0.10 (840 hom., 3193 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 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: 0.103 AC: 11452 AN: 111263 Hom.: 841 Cov.: 23 AF XY: 0.0948 AC XY: 3175 AN XY: 33495

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0209

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0629

Gnomad FIN AF: 0.00933

Gnomad MID AF: 0.0294

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.103 AC: 11467 AN: 111316 Hom.: 840 Cov.: 23 AF XY: 0.0951 AC XY: 3193 AN XY: 33558

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0209

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.0631

Gnomad4 FIN AF: 0.00933

Gnomad4 NFE AF: 0.0248

Gnomad4 OTH AF: 0.0808

Alfa AF: 0.0751 Hom.: 943

Bravo AF: 0.124

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.63
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs920833; hg19: chrX-15105601;