X-136579640-C-T

Variant names:

• chrX-136579640-C-T
• rs2807261

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 0.75 (22416 hom., 24653 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776
• 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=-0.91).

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: 0.752 AC: 83432 AN: 110903 Hom.: 22417 Cov.: 23

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.720

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: 0.752 AC: 83482 AN: 110958 Hom.: 22416 Cov.: 23 AF XY: 0.743 AC XY: 24653 AN XY: 33168

African (AFR) AF: 0.750 AC: 22934 AN: 30574

American (AMR) AF: 0.556 AC: 5790 AN: 10406

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2068 AN: 2635

East Asian (EAS) AF: 0.865 AC: 3053 AN: 3531

South Asian (SAS) AF: 0.674 AC: 1763 AN: 2615

European-Finnish (FIN) AF: 0.742 AC: 4349 AN: 5863

Middle Eastern (MID) AF: 0.836 AC: 179 AN: 214

European-Non Finnish (NFE) AF: 0.788 AC: 41710 AN: 52932

Other (OTH) AF: 0.725 AC: 1094 AN: 1510

Alfa AF: 0.723 Hom.: 16081

Bravo AF: 0.735

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.61
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2807261; hg19: chrX-135661799;