chrX-51600783-G-C

Variant names:

• chrX-51600783-G-C
• rs1541238

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 0.70 (19244 hom., 22865 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 4 publications found

ACMG classification

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

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

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: 0.697 AC: 77110 AN: 110657 Hom.: 19240 Cov.: 23

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

African (AFR) AF: 0.746 AC: 22717 AN: 30451

American (AMR) AF: 0.798 AC: 8338 AN: 10455

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2005 AN: 2644

East Asian (EAS) AF: 0.923 AC: 3224 AN: 3494

South Asian (SAS) AF: 0.724 AC: 1879 AN: 2595

European-Finnish (FIN) AF: 0.561 AC: 3270 AN: 5826

Middle Eastern (MID) AF: 0.662 AC: 141 AN: 213

European-Non Finnish (NFE) AF: 0.646 AC: 34139 AN: 52851

Other (OTH) AF: 0.703 AC: 1060 AN: 1508

Alfa AF: 0.669 Hom.: 5248

Bravo AF: 0.719

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
DANN	Benign	0.53
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs1541238; hg19: chrX-51343635;