X-51600783-G-C

Position:

• chrX-51600783-G-C

Variant summary

Our verdict is Likely benign. Variant got -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 0.70 (19244 hom., 22865 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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: 0.697 AC: 77110 AN: 110657 Hom.: 19240 Cov.: 23 AF XY: 0.694 AC XY: 22819 AN XY: 32883

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.700

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: 0.697 AC: 77158 AN: 110707 Hom.: 19244 Cov.: 23 AF XY: 0.694 AC XY: 22865 AN XY: 32943

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.703

Alfa AF: 0.669 Hom.: 5248

Bravo AF: 0.719

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
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: rs1541238; hg19: chrX-51343635;