X-143095139-T-C

Variant names:

• chrX-143095139-T-C
• rs2206024

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 0.459 in 111,024 control chromosomes in the GnomAD database, including 9,343 homozygotes. There are 14,882 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 0.46 (9343 hom., 14882 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 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: 0.459 AC: 50958 AN: 110975 Hom.: 9342 Cov.: 23 AF XY: 0.446 AC XY: 14826 AN XY: 33207

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.451

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.459 AC: 51009 AN: 111024 Hom.: 9343 Cov.: 23 AF XY: 0.447 AC XY: 14882 AN XY: 33266

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.462

Alfa AF: 0.382 Hom.: 8528

Bravo AF: 0.489

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2206024; hg19: chrX-142182925;