X-44055387-T-C

Variant names:

• chrX-44055387-T-C
• rs1375329

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 0.78 (23928 hom., 25659 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).

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: 0.782 AC: 86489 AN: 110613 Hom.: 23938 Cov.: 23

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.689

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.788

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: 0.782 AC: 86537 AN: 110671 Hom.: 23928 Cov.: 23 AF XY: 0.781 AC XY: 25659 AN XY: 32871

African (AFR) AF: 0.860 AC: 26177 AN: 30424

American (AMR) AF: 0.785 AC: 8138 AN: 10369

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 1975 AN: 2628

East Asian (EAS) AF: 0.895 AC: 3134 AN: 3503

South Asian (SAS) AF: 0.809 AC: 2119 AN: 2620

European-Finnish (FIN) AF: 0.720 AC: 4193 AN: 5826

Middle Eastern (MID) AF: 0.679 AC: 146 AN: 215

European-Non Finnish (NFE) AF: 0.738 AC: 39035 AN: 52903

Other (OTH) AF: 0.785 AC: 1181 AN: 1504

Alfa AF: 0.760 Hom.: 81181

Bravo AF: 0.793

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	4.2
DANN	Benign	0.64
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1375329; hg19: chrX-43914633;