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).

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: 0.592 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 v4.3

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;