chrX-66053345-T-G

Variant names:

• chrX-66053345-T-G
• rs599958

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 0.65 (12871 hom., 2525 hem., cov: 9)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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: 0.653 AC: 35913 AN: 55024 Hom.: 12864 Cov.: 9

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.685

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: 0.652 AC: 35941 AN: 55103 Hom.: 12871 Cov.: 9 AF XY: 0.300 AC XY: 2525 AN XY: 8419

African (AFR) AF: 0.414 AC: 7736 AN: 18672

American (AMR) AF: 0.629 AC: 2265 AN: 3599

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 1146 AN: 1373

East Asian (EAS) AF: 0.998 AC: 990 AN: 992

South Asian (SAS) AF: 0.713 AC: 345 AN: 484

European-Finnish (FIN) AF: 0.684 AC: 1113 AN: 1627

Middle Eastern (MID) AF: 0.607 AC: 37 AN: 61

European-Non Finnish (NFE) AF: 0.791 AC: 21602 AN: 27299

Other (OTH) AF: 0.687 AC: 435 AN: 633

Alfa AF: 0.749 Hom.: 4733

Bravo AF: 0.773

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	10
DANN	Benign	0.41
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs599958; hg19: chrX-65273187;