rs10521647

chrX-15059958-G-A

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 0.0645 in 111,438 control chromosomes in the GnomAD database, including 272 homozygotes. There are 2,025 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 0.064 (272 hom., 2025 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.148 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: 0.0645 AC: 7183 AN: 111384 Hom.: 273 Cov.: 22 AF XY: 0.0600 AC XY: 2017 AN XY: 33616

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.0606

Gnomad FIN AF: 0.00890

Gnomad MID AF: 0.0211

Gnomad NFE AF: 0.0244

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0645 AC: 7184 AN: 111438 Hom.: 272 Cov.: 22 AF XY: 0.0601 AC XY: 2025 AN XY: 33680

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.00890

Gnomad4 NFE AF: 0.0244

Gnomad4 OTH AF: 0.0533

Alfa AF: 0.0584 Hom.: 685

Bravo AF: 0.0788

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.3
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521647; hg19: chrX-15078080; COSMIC: COSV56546804;