X-55366646-T-C

Variant names:

• chrX-55366646-T-C
• rs4240023

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 0.85 (29381 hom., 28355 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).

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: 0.851 AC: 94266 AN: 110826 Hom.: 29390 Cov.: 23 AF XY: 0.857 AC XY: 28300 AN XY: 33040

Gnomad AFR AF: 0.543

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.975

Gnomad OTH AF: 0.863

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: 0.851 AC: 94304 AN: 110875 Hom.: 29381 Cov.: 23 AF XY: 0.857 AC XY: 28355 AN XY: 33099

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.945

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.944

Gnomad4 FIN AF: 0.994

Gnomad4 NFE AF: 0.975

Gnomad4 OTH AF: 0.865

Alfa AF: 0.827 Hom.: 4645

Bravo AF: 0.834

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.21
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: rs4240023; hg19: chrX-55393079;