X-51497226-C-T

Variant names:

• chrX-51497226-C-T
• rs28641581

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 0.65 (16938 hom., 20974 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.759
• 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=-0.81).

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: 0.655 AC: 71923 AN: 109819 Hom.: 16940 Cov.: 22

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.668

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: 0.655 AC: 71938 AN: 109871 Hom.: 16938 Cov.: 22 AF XY: 0.652 AC XY: 20974 AN XY: 32147

African (AFR) AF: 0.621 AC: 18745 AN: 30164

American (AMR) AF: 0.780 AC: 8104 AN: 10384

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 1965 AN: 2624

East Asian (EAS) AF: 0.921 AC: 3183 AN: 3455

South Asian (SAS) AF: 0.713 AC: 1801 AN: 2526

European-Finnish (FIN) AF: 0.553 AC: 3160 AN: 5710

Middle Eastern (MID) AF: 0.660 AC: 142 AN: 215

European-Non Finnish (NFE) AF: 0.636 AC: 33438 AN: 52616

Other (OTH) AF: 0.672 AC: 1011 AN: 1505

Alfa AF: 0.644 Hom.: 7962

Bravo AF: 0.674

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.88
PhyloP100		0.76

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs28641581; hg19: chrX-51240078;