X-5266661-C-T

Variant names:

• chrX-5266661-C-T
• rs6638512

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 0.56 (13068 hom., 18321 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

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: 0.564 AC: 62363 AN: 110630 Hom.: 13062 Cov.: 23

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.600

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.544

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: 0.564 AC: 62406 AN: 110679 Hom.: 13068 Cov.: 23 AF XY: 0.556 AC XY: 18321 AN XY: 32977

African (AFR) AF: 0.738 AC: 22499 AN: 30489

American (AMR) AF: 0.502 AC: 5200 AN: 10367

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1403 AN: 2633

East Asian (EAS) AF: 0.630 AC: 2212 AN: 3510

South Asian (SAS) AF: 0.383 AC: 1016 AN: 2654

European-Finnish (FIN) AF: 0.452 AC: 2626 AN: 5808

Middle Eastern (MID) AF: 0.603 AC: 129 AN: 214

European-Non Finnish (NFE) AF: 0.495 AC: 26134 AN: 52822

Other (OTH) AF: 0.544 AC: 820 AN: 1507

Alfa AF: 0.561 Hom.: 19887

Bravo AF: 0.578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.21
PhyloP100		-0.36

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: rs6638512;

hg19: chrX-5184702;

COSMIC: COSV56546748;