rs10126713

Variant names:

• chrX-100290386-T-C
• rs10126713

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 0.493 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.493 AC: 54296 AN: 110139 Hom.: 10114 Cov.: 22

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

African (AFR) AF: 0.563 AC: 17010 AN: 30232

American (AMR) AF: 0.460 AC: 4772 AN: 10381

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1417 AN: 2628

East Asian (EAS) AF: 0.156 AC: 544 AN: 3479

South Asian (SAS) AF: 0.253 AC: 655 AN: 2590

European-Finnish (FIN) AF: 0.398 AC: 2322 AN: 5834

Middle Eastern (MID) AF: 0.553 AC: 119 AN: 215

European-Non Finnish (NFE) AF: 0.503 AC: 26483 AN: 52648

Other (OTH) AF: 0.480 AC: 726 AN: 1512

Alfa AF: 0.500 Hom.: 66897

Bravo AF: 0.499

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.29
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs10126713; hg19: chrX-99545384;