X-146609682-T-C

Variant names:

• chrX-146609682-T-C
• rs11094364

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 0.79 (24126 hom., 25872 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• 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=-0.99).

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: 0.789 AC: 87049 AN: 110361 Hom.: 24121 Cov.: 23

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.730

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.770

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: 0.789 AC: 87095 AN: 110414 Hom.: 24126 Cov.: 23 AF XY: 0.792 AC XY: 25872 AN XY: 32674

African (AFR) AF: 0.812 AC: 24664 AN: 30361

American (AMR) AF: 0.842 AC: 8717 AN: 10353

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2166 AN: 2636

East Asian (EAS) AF: 0.793 AC: 2747 AN: 3466

South Asian (SAS) AF: 0.737 AC: 1902 AN: 2579

European-Finnish (FIN) AF: 0.778 AC: 4548 AN: 5843

Middle Eastern (MID) AF: 0.723 AC: 154 AN: 213

European-Non Finnish (NFE) AF: 0.769 AC: 40594 AN: 52793

Other (OTH) AF: 0.774 AC: 1162 AN: 1501

Alfa AF: 0.778 Hom.: 112090

Bravo AF: 0.794

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.42
PhyloP100		-1.1

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: rs11094364;

hg19: chrX-145691200;