X-51619759-G-A

Variant names:

• chrX-51619759-G-A
• rs7057039

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 0.72 (20593 hom., 23841 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• 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=-0.87).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.722 AC: 79967 AN: 110777 Hom.: 20589 Cov.: 23

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.660

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.715

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: 0.722 AC: 80023 AN: 110829 Hom.: 20593 Cov.: 23 AF XY: 0.721 AC XY: 23841 AN XY: 33047

African (AFR) AF: 0.804 AC: 24585 AN: 30568

American (AMR) AF: 0.810 AC: 8467 AN: 10459

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2003 AN: 2634

East Asian (EAS) AF: 0.926 AC: 3246 AN: 3505

South Asian (SAS) AF: 0.754 AC: 1953 AN: 2591

European-Finnish (FIN) AF: 0.559 AC: 3246 AN: 5806

Middle Eastern (MID) AF: 0.647 AC: 139 AN: 215

European-Non Finnish (NFE) AF: 0.657 AC: 34745 AN: 52851

Other (OTH) AF: 0.718 AC: 1093 AN: 1523

Alfa AF: 0.675 Hom.: 19466

Bravo AF: 0.746

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.84
DANN	Benign	0.75
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7057039; hg19: chrX-51362611;