X-135463627-T-C

Variant names:

• chrX-135463627-T-C
• rs4320696

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 (12639 hom., 18670 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799
• Publications: 0 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: 0.565 AC: 62798 AN: 111206 Hom.: 12631 Cov.: 23

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.461

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.533

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: 0.565 AC: 62816 AN: 111261 Hom.: 12639 Cov.: 23 AF XY: 0.557 AC XY: 18670 AN XY: 33497

African (AFR) AF: 0.557 AC: 17066 AN: 30627

American (AMR) AF: 0.644 AC: 6802 AN: 10557

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1402 AN: 2629

East Asian (EAS) AF: 0.482 AC: 1680 AN: 3488

South Asian (SAS) AF: 0.386 AC: 1035 AN: 2683

European-Finnish (FIN) AF: 0.530 AC: 3152 AN: 5949

Middle Eastern (MID) AF: 0.464 AC: 98 AN: 211

European-Non Finnish (NFE) AF: 0.573 AC: 30332 AN: 52909

Other (OTH) AF: 0.538 AC: 824 AN: 1532

Alfa AF: 0.568 Hom.: 4492

Bravo AF: 0.576

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.66
PhyloP100		0.80

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: rs4320696;

hg19: chrX-134597552;