chrX-117469443-T-C

Variant names:

• chrX-117469443-T-C
• rs2040962

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 0.61 (15364 hom., 20345 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

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: 0.614 AC: 67883 AN: 110632 Hom.: 15360 Cov.: 23

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.502

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.604

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: 0.614 AC: 67935 AN: 110687 Hom.: 15364 Cov.: 23 AF XY: 0.618 AC XY: 20345 AN XY: 32937

African (AFR) AF: 0.772 AC: 23501 AN: 30448

American (AMR) AF: 0.696 AC: 7226 AN: 10387

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1454 AN: 2629

East Asian (EAS) AF: 0.960 AC: 3364 AN: 3505

South Asian (SAS) AF: 0.823 AC: 2172 AN: 2639

European-Finnish (FIN) AF: 0.518 AC: 3055 AN: 5897

Middle Eastern (MID) AF: 0.502 AC: 107 AN: 213

European-Non Finnish (NFE) AF: 0.491 AC: 25919 AN: 52786

Other (OTH) AF: 0.610 AC: 918 AN: 1504

Alfa AF: 0.543 Hom.: 57108

Bravo AF: 0.637

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.35

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: rs2040962;

hg19: chrX-116603406;