X-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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;