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).

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: 0.534 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 v4.3

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;