chr11-104037513-A-ATAGAAGAGGCCCCCGAGAGTTTT
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001001711.3(DDI1):c.692_714dup(p.Gly239Ter) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,614,008 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
DDI1
NM_001001711.3 frameshift
NM_001001711.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.67
Genes affected
DDI1 (HGNC:18961): (DNA damage inducible 1 homolog 1) Predicted to enable aspartic-type endopeptidase activity. Involved in several processes, including cellular response to hydroxyurea; proteasomal protein catabolic process; and regulation of DNA stability. [provided by Alliance of Genome Resources, Apr 2022]
PDGFD (HGNC:30620): (platelet derived growth factor D) The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of this family are mitogenic factors for cells of mesenchymal origin and are characterized by a core motif of eight cysteines, seven of which are found in this factor. This gene product only forms homodimers and, therefore, does not dimerize with the other three family members. It differs from alpha and beta members of this family in having an unusual N-terminal domain, the CUB domain. Two splice variants have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDI1 | NM_001001711.3 | c.692_714dup | p.Gly239Ter | frameshift_variant | 1/1 | ENST00000302259.5 | |
PDGFD | NM_025208.5 | c.125-37259_125-37258insAAAACTCTCGGGGGCCTCTTCTA | intron_variant | ENST00000393158.7 | |||
PDGFD | NM_033135.4 | c.125-37277_125-37276insAAAACTCTCGGGGGCCTCTTCTA | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDI1 | ENST00000302259.5 | c.692_714dup | p.Gly239Ter | frameshift_variant | 1/1 | NM_001001711.3 | P1 | ||
PDGFD | ENST00000393158.7 | c.125-37259_125-37258insAAAACTCTCGGGGGCCTCTTCTA | intron_variant | 1 | NM_025208.5 | P1 | |||
PDGFD | ENST00000302251.9 | c.125-37277_125-37276insAAAACTCTCGGGGGCCTCTTCTA | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251242Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135850
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GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727228
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Premature ovarian insufficiency Uncertain:1
Uncertain significance, no assertion criteria provided | research | Reproductive Development, Murdoch Childrens Research Institute | Jan 10, 2018 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at