X-145887710-C-T

Variant names:

• chrX-145887710-C-T
• rs12558359

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 0.424 in 109,858 control chromosomes in the GnomAD database, including 7,824 homozygotes. There are 13,142 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 0.42 (7824 hom., 13142 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.424 AC: 46580 AN: 109816 Hom.: 7825 Cov.: 22

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.0667

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.470

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.424 AC: 46607 AN: 109858 Hom.: 7824 Cov.: 22 AF XY: 0.408 AC XY: 13142 AN XY: 32206

African (AFR) AF: 0.589 AC: 17781 AN: 30209

American (AMR) AF: 0.277 AC: 2848 AN: 10273

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1188 AN: 2621

East Asian (EAS) AF: 0.0664 AC: 231 AN: 3480

South Asian (SAS) AF: 0.294 AC: 775 AN: 2632

European-Finnish (FIN) AF: 0.326 AC: 1857 AN: 5702

Middle Eastern (MID) AF: 0.469 AC: 98 AN: 209

European-Non Finnish (NFE) AF: 0.397 AC: 20848 AN: 52576

Other (OTH) AF: 0.383 AC: 571 AN: 1489

Alfa AF: 0.429 Hom.: 20360

Bravo AF: 0.427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.4
DANN	Benign	0.63
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs12558359; hg19: chrX-144969228;