rs7057039

Positions:

• chrX-51619759-G-A
• chrX-51619759-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 0.72 (20593 hom., 23841 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.722 AC: 79967 AN: 110777 Hom.: 20589 Cov.: 23 AF XY: 0.721 AC XY: 23786 AN XY: 32985

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

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.718

Alfa AF: 0.682 Hom.: 11595

Bravo AF: 0.746

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7057039; hg19: chrX-51362611;