2-199925310-TTTTAA-T
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Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_153689.6(C2orf69):c.588_592del(p.Asn196LysfsTer4) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000868 in 1,612,486 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000082 ( 0 hom. )
Consequence
C2orf69
NM_153689.6 frameshift
NM_153689.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.18
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.497 CDS is truncated, and there are 2 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 2-199925310-TTTTAA-T is Pathogenic according to our data. Variant chr2-199925310-TTTTAA-T is described in ClinVar as [Pathogenic]. Clinvar id is 1177456.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-199925310-TTTTAA-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C2orf69 | NM_153689.6 | c.588_592del | p.Asn196LysfsTer4 | frameshift_variant | 2/2 | ENST00000319974.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C2orf69 | ENST00000319974.6 | c.588_592del | p.Asn196LysfsTer4 | frameshift_variant | 2/2 | 1 | NM_153689.6 | P1 | |
C2orf69 | ENST00000491721.1 | n.466+13545_466+13549del | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000120 AC: 3AN: 248974Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135078
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GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460252Hom.: 0 AF XY: 0.00000551 AC XY: 4AN XY: 726458
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74370
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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 12, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at