X-145231305-A-G

Variant names:

• chrX-145231305-A-G
• rs5920468

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 0.54 (11747 hom., 17782 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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: 0.540 AC: 59693 AN: 110506 Hom.: 11751 Cov.: 23

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.522

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: 0.540 AC: 59737 AN: 110558 Hom.: 11747 Cov.: 23 AF XY: 0.542 AC XY: 17782 AN XY: 32824

African (AFR) AF: 0.603 AC: 18313 AN: 30388

American (AMR) AF: 0.667 AC: 6897 AN: 10345

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1037 AN: 2630

East Asian (EAS) AF: 0.846 AC: 2950 AN: 3485

South Asian (SAS) AF: 0.628 AC: 1630 AN: 2595

European-Finnish (FIN) AF: 0.535 AC: 3140 AN: 5866

Middle Eastern (MID) AF: 0.406 AC: 86 AN: 212

European-Non Finnish (NFE) AF: 0.466 AC: 24627 AN: 52862

Other (OTH) AF: 0.523 AC: 788 AN: 1506

Alfa AF: 0.483 Hom.: 23712

Bravo AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.47
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs5920468; hg19: chrX-144312825;