chrX-122334492-C-T

Variant names:

• chrX-122334492-C-T
• rs10521708

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 0.0984 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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

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

African (AFR) AF: 0.302 AC: 9246 AN: 30585

American (AMR) AF: 0.0570 AC: 599 AN: 10512

Ashkenazi Jewish (ASJ) AF: 0.0227 AC: 60 AN: 2645

East Asian (EAS) AF: 0.000282 AC: 1 AN: 3547

South Asian (SAS) AF: 0.00670 AC: 18 AN: 2685

European-Finnish (FIN) AF: 0.00563 AC: 34 AN: 6035

Middle Eastern (MID) AF: 0.0930 AC: 20 AN: 215

European-Non Finnish (NFE) AF: 0.0163 AC: 864 AN: 53088

Other (OTH) AF: 0.0836 AC: 128 AN: 1532

Alfa AF: 0.0458 Hom.: 4715

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
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs10521708; hg19: chrX-121468345;