X-132016786-T-A

Variant names:

• chrX-132016786-T-A
• rs2748723

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 0.94 (34670 hom., 29075 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.536
• 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=-0.89).

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: 0.938 AC: 102224 AN: 108977 Hom.: 34668 Cov.: 21

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.944

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.918

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: 0.938 AC: 102275 AN: 109025 Hom.: 34670 Cov.: 21 AF XY: 0.930 AC XY: 29075 AN XY: 31271

African (AFR) AF: 0.989 AC: 29613 AN: 29946

American (AMR) AF: 0.877 AC: 8894 AN: 10140

Ashkenazi Jewish (ASJ) AF: 0.928 AC: 2434 AN: 2623

East Asian (EAS) AF: 0.602 AC: 2076 AN: 3449

South Asian (SAS) AF: 0.837 AC: 2077 AN: 2481

European-Finnish (FIN) AF: 0.920 AC: 5062 AN: 5501

Middle Eastern (MID) AF: 0.953 AC: 202 AN: 212

European-Non Finnish (NFE) AF: 0.950 AC: 49902 AN: 52519

Other (OTH) AF: 0.917 AC: 1354 AN: 1477

Alfa AF: 0.938 Hom.: 7923

Bravo AF: 0.934

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.66
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs2748723; hg19: chrX-131150814;