X-127010099-T-C

Variant names:

• chrX-127010099-T-C
• rs204340

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 1.0 (38869 hom., 31874 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 1.00 AC: 109587 AN: 109587 Hom.: 38874 Cov.: 22

Gnomad AFR AF: 1.00

Gnomad AMI AF: 1.00

Gnomad AMR AF: 1.00

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 1.00

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: 1.00 AC: 109612 AN: 109612 Hom.: 38869 Cov.: 22 AF XY: 1.00 AC XY: 31874 AN XY: 31874

African (AFR) AF: 1.00 AC: 30269 AN: 30269

American (AMR) AF: 1.00 AC: 10321 AN: 10321

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2625 AN: 2625

East Asian (EAS) AF: 1.00 AC: 3456 AN: 3456

South Asian (SAS) AF: 1.00 AC: 2557 AN: 2557

European-Finnish (FIN) AF: 1.00 AC: 5379 AN: 5379

Middle Eastern (MID) AF: 1.00 AC: 209 AN: 209

European-Non Finnish (NFE) AF: 1.00 AC: 52620 AN: 52620

Other (OTH) AF: 1.00 AC: 1494 AN: 1494

Alfa AF: 1.00 Hom.: 8564

Bravo AF: 1.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs204340; hg19: chrX-126144082;