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).

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: 0.938 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 v4.3

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;