X-114579649-C-T

Variant names:

• chrX-114579649-C-T
• rs508865

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 0.65 (16510 hom., 20996 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• 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=-0.84).

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: 0.650 AC: 71436 AN: 109956 Hom.: 16517 Cov.: 23

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.676

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: 0.649 AC: 71437 AN: 110006 Hom.: 16510 Cov.: 23 AF XY: 0.650 AC XY: 20996 AN XY: 32322

African (AFR) AF: 0.595 AC: 18013 AN: 30266

American (AMR) AF: 0.644 AC: 6650 AN: 10324

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 1654 AN: 2616

East Asian (EAS) AF: 0.833 AC: 2887 AN: 3466

South Asian (SAS) AF: 0.618 AC: 1591 AN: 2575

European-Finnish (FIN) AF: 0.728 AC: 4190 AN: 5758

Middle Eastern (MID) AF: 0.619 AC: 133 AN: 215

European-Non Finnish (NFE) AF: 0.661 AC: 34767 AN: 52604

Other (OTH) AF: 0.677 AC: 1024 AN: 1513

Alfa AF: 0.653 Hom.: 5755

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.65
PhyloP100		-0.16

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: rs508865; hg19: chrX-113814115;