4-146909091-TCCTCC-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_031956.4(TTC29):c.330_334del(p.Glu111AlafsTer3) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000161 in 1,613,798 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
TTC29
NM_031956.4 frameshift
NM_031956.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.41
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 4-146909091-TCCTCC-T is Pathogenic according to our data. Variant chr4-146909091-TCCTCC-T is described in ClinVar as [Pathogenic]. Clinvar id is 805957.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr4-146909091-TCCTCC-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC29 | NM_031956.4 | c.330_334del | p.Glu111AlafsTer3 | frameshift_variant | 5/13 | ENST00000325106.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC29 | ENST00000325106.9 | c.330_334del | p.Glu111AlafsTer3 | frameshift_variant | 5/13 | 1 | NM_031956.4 | P4 | |
TTC29 | ENST00000508306.5 | c.330_334del | p.Glu111AlafsTer3 | frameshift_variant, NMD_transcript_variant | 5/14 | 1 | |||
TTC29 | ENST00000504425.5 | c.330_334del | p.Glu111AlafsTer3 | frameshift_variant | 5/13 | 5 | A1 | ||
TTC29 | ENST00000513335.5 | c.408_412del | p.Glu137AlafsTer3 | frameshift_variant | 6/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152160Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248594Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134816
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GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461638Hom.: 0 AF XY: 0.0000138 AC XY: 10AN XY: 727094
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Spermatogenic failure 42 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 23, 2020 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at