rs10126713

chrX-100290386-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;