X-146265919-G-T

Variant names:

• chrX-146265919-G-T
• rs4263905

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 0.59 (14091 hom., 18701 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 2 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).

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: 0.592 AC: 65053 AN: 109877 Hom.: 14104 Cov.: 23

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.569

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: 0.592 AC: 65067 AN: 109934 Hom.: 14091 Cov.: 23 AF XY: 0.580 AC XY: 18701 AN XY: 32258

African (AFR) AF: 0.658 AC: 19845 AN: 30180

American (AMR) AF: 0.453 AC: 4660 AN: 10293

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1505 AN: 2632

East Asian (EAS) AF: 0.658 AC: 2254 AN: 3423

South Asian (SAS) AF: 0.558 AC: 1450 AN: 2597

European-Finnish (FIN) AF: 0.540 AC: 3126 AN: 5788

Middle Eastern (MID) AF: 0.545 AC: 116 AN: 213

European-Non Finnish (NFE) AF: 0.588 AC: 30960 AN: 52646

Other (OTH) AF: 0.566 AC: 844 AN: 1491

Alfa AF: 0.555 Hom.: 18790

Bravo AF: 0.585

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0060
DANN	Benign	0.53
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4263905; hg19: chrX-145347437;