chr2-99155118-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_145199.3(LIPT1):c.-2+67C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00562 in 450,498 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.013 ( 37 hom., cov: 34)
Exomes 𝑓: 0.0019 ( 8 hom. )
Consequence
LIPT1
NM_145199.3 intron
NM_145199.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.932
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 2-99155118-C-T is Benign according to our data. Variant chr2-99155118-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1196049.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1954/152326) while in subpopulation AFR AF= 0.043 (1787/41582). AF 95% confidence interval is 0.0413. There are 37 homozygotes in gnomad4. There are 929 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 37 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPT1 | NM_145199.3 | c.-2+67C>T | intron_variant | ENST00000651691.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPT1 | ENST00000651691.1 | c.-2+67C>T | intron_variant | NM_145199.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0128 AC: 1955AN: 152208Hom.: 37 Cov.: 34
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GnomAD4 exome AF: 0.00194 AC: 579AN: 298172Hom.: 8 Cov.: 0 AF XY: 0.00153 AC XY: 260AN XY: 169784
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GnomAD4 genome ? AF: 0.0128 AC: 1954AN: 152326Hom.: 37 Cov.: 34 AF XY: 0.0125 AC XY: 929AN XY: 74488
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 29, 2018 | - - |
Computational scores
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BayesDel_noAF
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Cadd
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Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at