chr2-199911748-CTCT-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4_SupportingPP5
The NM_153689.6(C2orf69):c.311_313del(p.Leu104_Tyr105delinsHis) variant causes a inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
C2orf69
NM_153689.6 inframe_deletion
NM_153689.6 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.88
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_153689.6. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant 2-199911748-CTCT-C is Pathogenic according to our data. Variant chr2-199911748-CTCT-C is described in ClinVar as [Pathogenic]. Clinvar id is 1177457.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-199911748-CTCT-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C2orf69 | NM_153689.6 | c.311_313del | p.Leu104_Tyr105delinsHis | inframe_deletion | 1/2 | ENST00000319974.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C2orf69 | ENST00000319974.6 | c.311_313del | p.Leu104_Tyr105delinsHis | inframe_deletion | 1/2 | 1 | NM_153689.6 | P1 | |
C2orf69 | ENST00000491721.1 | n.444_446del | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Combined oxidative phosphorylation deficiency 53 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 09, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
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Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.