X-122334492-C-T

Variant names:

• chrX-122334492-C-T
• rs10521708

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 0.0984 in 111,530 control chromosomes in the GnomAD database, including 1,099 homozygotes. There are 2,998 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 0.098 (1099 hom., 2998 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 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: 0.0982 AC: 10944 AN: 111482 Hom.: 1099 Cov.: 22 AF XY: 0.0882 AC XY: 2971 AN XY: 33696

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.00729

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.0227

Gnomad EAS AF: 0.000281

Gnomad SAS AF: 0.00668

Gnomad FIN AF: 0.00563

Gnomad MID AF: 0.0847

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0846

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

GnomAD4 genome AF: 0.0984 AC: 10975 AN: 111530 Hom.: 1099 Cov.: 22 AF XY: 0.0888 AC XY: 2998 AN XY: 33754

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.0570

Gnomad4 ASJ AF: 0.0227

Gnomad4 EAS AF: 0.000282

Gnomad4 SAS AF: 0.00670

Gnomad4 FIN AF: 0.00563

Gnomad4 NFE AF: 0.0163

Gnomad4 OTH AF: 0.0836

Alfa AF: 0.0221 Hom.: 1543

Bravo AF: 0.112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521708; hg19: chrX-121468345;