X-117387453-G-T

Variant names:

• chrX-117387453-G-T
• rs2190288

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.53 (11403 hom., 17456 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 1 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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: 0.534 AC: 58841 AN: 110148 Hom.: 11399 Cov.: 23

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.476

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.526

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.534 AC: 58882 AN: 110200 Hom.: 11403 Cov.: 23 AF XY: 0.536 AC XY: 17456 AN XY: 32552

African (AFR) AF: 0.665 AC: 20226 AN: 30435

American (AMR) AF: 0.436 AC: 4512 AN: 10344

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1362 AN: 2622

East Asian (EAS) AF: 0.574 AC: 1979 AN: 3447

South Asian (SAS) AF: 0.683 AC: 1764 AN: 2584

European-Finnish (FIN) AF: 0.527 AC: 3031 AN: 5751

Middle Eastern (MID) AF: 0.466 AC: 97 AN: 208

European-Non Finnish (NFE) AF: 0.472 AC: 24826 AN: 52637

Other (OTH) AF: 0.530 AC: 802 AN: 1514

Alfa AF: 0.497 Hom.: 4190

Bravo AF: 0.527

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.45
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2190288; hg19: chrX-116521416;