rs10521834

Variant names:

• chrX-142993238-C-T
• rs10521834

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 0.131 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.131 AC: 14393 AN: 109962 Hom.: 956 Cov.: 22

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

African (AFR) AF: 0.107 AC: 3238 AN: 30302

American (AMR) AF: 0.366 AC: 3741 AN: 10232

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 130 AN: 2622

East Asian (EAS) AF: 0.308 AC: 1063 AN: 3454

South Asian (SAS) AF: 0.0792 AC: 207 AN: 2615

European-Finnish (FIN) AF: 0.156 AC: 912 AN: 5841

Middle Eastern (MID) AF: 0.0372 AC: 8 AN: 215

European-Non Finnish (NFE) AF: 0.0906 AC: 4761 AN: 52561

Other (OTH) AF: 0.154 AC: 230 AN: 1497

Alfa AF: 0.118 Hom.: 5188

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
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs10521834; hg19: chrX-142081024;