X-146265919-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS2: High Homozygotes in GnomAd at 14104 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.592 AC: 65053 AN: 109877 Hom.: 14104 Cov.: 23 AF XY: 0.580 AC XY: 18666 AN XY: 32191

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

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.566

Alfa AF: 0.540 Hom.: 11393

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4263905; hg19: chrX-145347437;