chr2-99155507-C-A
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_145199.3(LIPT1):c.-2+456C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00774 in 455,994 control chromosomes in the GnomAD database, including 150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0081 ( 48 hom., cov: 32)
Exomes 𝑓: 0.0076 ( 102 hom. )
Consequence
LIPT1
NM_145199.3 intron
NM_145199.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.622
Genes affected
LIPT1 (HGNC:29569): (lipoyltransferase 1) The process of transferring lipoic acid to proteins is a two-step process. The first step is the activation of lipoic acid by lipoate-activating enzyme to form lipoyl-AMP. For the second step, the protein encoded by this gene transfers the lipoyl moiety to apoproteins. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 13. Read-through transcription also exists between this gene and the neighboring downstream mitochondrial ribosomal protein L30 (MRPL30) gene. [provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 2-99155507-C-A is Benign according to our data. Variant chr2-99155507-C-A is described in ClinVar as [Benign]. Clinvar id is 1268497.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0685 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT1 | NM_145199.3 | c.-2+456C>A | intron_variant | ENST00000651691.1 | NP_660200.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPT1 | ENST00000651691.1 | c.-2+456C>A | intron_variant | NM_145199.3 | ENSP00000498546.1 | |||||
ENSG00000273155 | ENST00000410042.1 | c.-154+456C>A | intron_variant | 2 | ENSP00000387111.1 | |||||
ENSG00000241962 | ENST00000424491.5 | n.63+4988C>A | intron_variant | 2 | ENSP00000390891.1 |
Frequencies
GnomAD3 genomes AF: 0.00807 AC: 1227AN: 152096Hom.: 47 Cov.: 32
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GnomAD3 exomes AF: 0.0155 AC: 2030AN: 130692Hom.: 92 AF XY: 0.0117 AC XY: 835AN XY: 71328
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GnomAD4 exome AF: 0.00756 AC: 2296AN: 303780Hom.: 102 Cov.: 0 AF XY: 0.00564 AC XY: 975AN XY: 173002
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GnomAD4 genome AF: 0.00809 AC: 1232AN: 152214Hom.: 48 Cov.: 32 AF XY: 0.00899 AC XY: 669AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 22, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -25
Find out detailed SpliceAI scores and Pangolin per-transcript scores at