2-99156738-T-G
Position:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_145199.3(LIPT1):c.-2+1687T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,134 control chromosomes in the GnomAD database, including 29,800 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.62 ( 29799 hom., cov: 33)
Exomes 𝑓: 1.0 ( 1 hom. )
Consequence
LIPT1
NM_145199.3 intron
NM_145199.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.604
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
Variant 2-99156738-T-G is Benign according to our data. Variant chr2-99156738-T-G is described in ClinVar as [Benign]. Clinvar id is 1258591.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT1 | NM_145199.3 | c.-2+1687T>G | 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+1687T>G | intron_variant | NM_145199.3 | ENSP00000498546 | P1 |
Frequencies
GnomAD3 genomes AF: 0.621 AC: 94413AN: 152014Hom.: 29761 Cov.: 33
GnomAD3 genomes
AF:
AC:
94413
AN:
152014
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 1.00 AC: 2AN: 2Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2AN XY: 2
GnomAD4 exome
AF:
AC:
2
AN:
2
Hom.:
Cov.:
0
AF XY:
AC XY:
2
AN XY:
2
Gnomad4 FIN exome
AF:
GnomAD4 genome AF: 0.621 AC: 94498AN: 152132Hom.: 29799 Cov.: 33 AF XY: 0.619 AC XY: 46079AN XY: 74396
GnomAD4 genome
AF:
AC:
94498
AN:
152132
Hom.:
Cov.:
33
AF XY:
AC XY:
46079
AN XY:
74396
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2512
AN:
3478
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 | clinical testing | GeneDx | Jun 29, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at