rs10521737

Variant names:

• chrX-126153090-G-A
• rs10521737

Your query was ambiguous. Multiple possible variants found:

• chrX-126153090-G-A
• chrX-126153090-G-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 0.0573 in 111,505 control chromosomes in the GnomAD database, including 170 homozygotes. There are 1,829 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 0.057 (170 hom., 1829 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.681

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 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: 0.0573 AC: 6386 AN: 111458 Hom.: 170 Cov.: 22 AF XY: 0.0542 AC XY: 1828 AN XY: 33748

Gnomad AFR AF: 0.0618

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0720

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0116

Gnomad MID AF: 0.0460

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0573 AC: 6384 AN: 111505 Hom.: 170 Cov.: 22 AF XY: 0.0541 AC XY: 1829 AN XY: 33805

Gnomad4 AFR AF: 0.0617

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.0625

Gnomad4 EAS AF: 0.0716

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.0116

Gnomad4 NFE AF: 0.0559

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0669 Hom.: 1186

Bravo AF: 0.0589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521737; hg19: chrX-125287073;