2-99156738-T-G

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.604
Variant links:
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
LIPT1NM_145199.3 linkuse as main transcriptc.-2+1687T>G intron_variant ENST00000651691.1 NP_660200.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LIPT1ENST00000651691.1 linkuse as main transcriptc.-2+1687T>G intron_variant NM_145199.3 ENSP00000498546 P1

Frequencies

GnomAD3 genomes
AF:
0.621
AC:
94413
AN:
152014
Hom.:
29761
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.538
Gnomad AMI
AF:
0.729
Gnomad AMR
AF:
0.633
Gnomad ASJ
AF:
0.650
Gnomad EAS
AF:
0.884
Gnomad SAS
AF:
0.630
Gnomad FIN
AF:
0.567
Gnomad MID
AF:
0.769
Gnomad NFE
AF:
0.652
Gnomad OTH
AF:
0.661
GnomAD4 exome
AF:
1.00
AC:
2
AN:
2
Hom.:
1
Cov.:
0
AF XY:
1.00
AC XY:
2
AN XY:
2
show subpopulations
Gnomad4 FIN exome
AF:
1.00
GnomAD4 genome
AF:
0.621
AC:
94498
AN:
152132
Hom.:
29799
Cov.:
33
AF XY:
0.619
AC XY:
46079
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.538
Gnomad4 AMR
AF:
0.632
Gnomad4 ASJ
AF:
0.650
Gnomad4 EAS
AF:
0.884
Gnomad4 SAS
AF:
0.629
Gnomad4 FIN
AF:
0.567
Gnomad4 NFE
AF:
0.652
Gnomad4 OTH
AF:
0.665
Alfa
AF:
0.652
Hom.:
50869
Bravo
AF:
0.621
Asia WGS
AF:
0.722
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 submitterclinical testingGeneDxJun 29, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
2.2
DANN
Benign
0.80

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2516829; hg19: chr2-99773201; API