X-114583441-G-T

Variant names:

• chrX-114583441-G-T
• rs521018

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 0.66 (16966 hom., 21596 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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: 0.658 AC: 72741 AN: 110604 Hom.: 16977 Cov.: 23

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.688

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: 0.657 AC: 72743 AN: 110658 Hom.: 16966 Cov.: 23 AF XY: 0.656 AC XY: 21596 AN XY: 32910

African (AFR) AF: 0.626 AC: 19004 AN: 30373

American (AMR) AF: 0.653 AC: 6866 AN: 10513

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 1671 AN: 2631

East Asian (EAS) AF: 0.848 AC: 2918 AN: 3442

South Asian (SAS) AF: 0.597 AC: 1566 AN: 2621

European-Finnish (FIN) AF: 0.724 AC: 4260 AN: 5881

Middle Eastern (MID) AF: 0.633 AC: 133 AN: 210

European-Non Finnish (NFE) AF: 0.658 AC: 34757 AN: 52808

Other (OTH) AF: 0.689 AC: 1037 AN: 1506

Alfa AF: 0.646 Hom.: 69054

Bravo AF: 0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.39
PhyloP100		-0.052

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: rs521018;

hg19: chrX-113817908;