rs10521834

Positions:

• chrX-142993238-C-T

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 0.131 in 110,015 control chromosomes in the GnomAD database, including 958 homozygotes. There are 4,442 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 0.13 (958 hom., 4442 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 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: 0.131 AC: 14393 AN: 109962 Hom.: 956 Cov.: 22 AF XY: 0.137 AC XY: 4432 AN XY: 32420

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.0789

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0381

Gnomad NFE AF: 0.0906

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.131 AC: 14414 AN: 110015 Hom.: 958 Cov.: 22 AF XY: 0.137 AC XY: 4442 AN XY: 32483

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.0792

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.0906

Gnomad4 OTH AF: 0.154

Alfa AF: 0.117 Hom.: 4468

Bravo AF: 0.158

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521834; hg19: chrX-142081024;