rs5945572

Variant names:

• chrX-51486831-A-G
• rs5945572

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 0.68 (18424 hom., 22265 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 90 publications found

ACMG classification

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

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

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: 0.684 AC: 75450 AN: 110377 Hom.: 18422 Cov.: 23

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

African (AFR) AF: 0.715 AC: 21655 AN: 30293

American (AMR) AF: 0.787 AC: 8174 AN: 10384

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 1988 AN: 2628

East Asian (EAS) AF: 0.924 AC: 3225 AN: 3491

South Asian (SAS) AF: 0.710 AC: 1847 AN: 2601

European-Finnish (FIN) AF: 0.575 AC: 3355 AN: 5838

Middle Eastern (MID) AF: 0.689 AC: 146 AN: 212

European-Non Finnish (NFE) AF: 0.638 AC: 33681 AN: 52806

Other (OTH) AF: 0.692 AC: 1043 AN: 1507

Alfa AF: 0.666 Hom.: 99335

Bravo AF: 0.705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.046
DANN	Benign	0.43
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs5945572; hg19: chrX-51229683;