rs10126713

Variant names:

• chrX-100290386-T-C
• rs10126713

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 0.493 in 110,195 control chromosomes in the GnomAD database, including 10,115 homozygotes. There are 15,396 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 0.49 (10115 hom., 15396 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 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: 0.493 AC: 54296 AN: 110139 Hom.: 10114 Cov.: 22 AF XY: 0.474 AC XY: 15358 AN XY: 32429

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.493 AC: 54333 AN: 110195 Hom.: 10115 Cov.: 22 AF XY: 0.474 AC XY: 15396 AN XY: 32495

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.480

Alfa AF: 0.495 Hom.: 49869

Bravo AF: 0.499

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10126713; hg19: chrX-99545384;