X-146271035-T-C

Variant names:

• chrX-146271035-T-C
• rs5920061

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 0.59 (14117 hom., 19321 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• 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=-0.92).

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: 0.594 AC: 65802 AN: 110750 Hom.: 14128 Cov.: 23

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.572

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.571

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: 0.594 AC: 65801 AN: 110799 Hom.: 14117 Cov.: 23 AF XY: 0.584 AC XY: 19321 AN XY: 33073

African (AFR) AF: 0.657 AC: 19963 AN: 30398

American (AMR) AF: 0.454 AC: 4758 AN: 10482

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1500 AN: 2626

East Asian (EAS) AF: 0.690 AC: 2396 AN: 3472

South Asian (SAS) AF: 0.591 AC: 1550 AN: 2622

European-Finnish (FIN) AF: 0.546 AC: 3239 AN: 5935

Middle Eastern (MID) AF: 0.553 AC: 119 AN: 215

European-Non Finnish (NFE) AF: 0.588 AC: 31102 AN: 52853

Other (OTH) AF: 0.567 AC: 862 AN: 1520

Alfa AF: 0.582 Hom.: 22345

Bravo AF: 0.586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.37
PhyloP100		-0.54

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: rs5920061;

hg19: chrX-145352553;