rs10521647

Variant names:

• chrX-15059958-G-A
• rs10521647

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 0.0645 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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 rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 7183 AN: 111384 Hom.: 273 Cov.: 22

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

African (AFR) AF: 0.119 AC: 3630 AN: 30626

American (AMR) AF: 0.129 AC: 1353 AN: 10504

Ashkenazi Jewish (ASJ) AF: 0.0208 AC: 55 AN: 2645

East Asian (EAS) AF: 0.159 AC: 552 AN: 3477

South Asian (SAS) AF: 0.0608 AC: 159 AN: 2616

European-Finnish (FIN) AF: 0.00890 AC: 54 AN: 6066

Middle Eastern (MID) AF: 0.0231 AC: 5 AN: 216

European-Non Finnish (NFE) AF: 0.0244 AC: 1295 AN: 53083

Other (OTH) AF: 0.0533 AC: 81 AN: 1520

Alfa AF: 0.0554 Hom.: 741

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
PhyloP100		0.38

Splicing

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

Other links and lift over

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