X-15087479-T-C

Variant names:

• chrX-15087479-T-C
• rs920833

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 0.103 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
• Publications: 0 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.103 AC: 11452 AN: 111263 Hom.: 841 Cov.: 23

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

African (AFR) AF: 0.248 AC: 7574 AN: 30491

American (AMR) AF: 0.149 AC: 1563 AN: 10478

Ashkenazi Jewish (ASJ) AF: 0.0209 AC: 55 AN: 2636

East Asian (EAS) AF: 0.173 AC: 608 AN: 3523

South Asian (SAS) AF: 0.0631 AC: 165 AN: 2615

European-Finnish (FIN) AF: 0.00933 AC: 56 AN: 6001

Middle Eastern (MID) AF: 0.0323 AC: 7 AN: 217

European-Non Finnish (NFE) AF: 0.0248 AC: 1316 AN: 53146

Other (OTH) AF: 0.0808 AC: 123 AN: 1523

Alfa AF: 0.0740 Hom.: 1063

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs920833; hg19: chrX-15105601;