rs5945572

Positions:

• chrX-51486831-A-G

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 0.68 (18424 hom., 22265 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

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: 0.684 AC: 75450 AN: 110377 Hom.: 18422 Cov.: 23 AF XY: 0.681 AC XY: 22209 AN XY: 32625

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.705

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.688

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: 0.684 AC: 75506 AN: 110434 Hom.: 18424 Cov.: 23 AF XY: 0.681 AC XY: 22265 AN XY: 32692

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.692

Alfa AF: 0.661 Hom.: 69503

Bravo AF: 0.705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.046
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5945572; hg19: chrX-51229683;