Variant 2-99155127-G-T details in Genebe, Genetics Data Aggregator

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+76G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 446,016 control chromosomes in the GnomAD database, including 84,745 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 26506 hom., cov: 33)

Exomes 𝑓: 0.63 ( 58239 hom. )

Consequence

LIPT1
NM_145199.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.531

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]

LIPT1 links:

ENSG00000273155 (HGNC:):

ENSG00000273155 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 2-99155127-G-T is Benign according to our data. Variant chr2-99155127-G-T is described in ClinVar as [Benign]. Clinvar id is 1294394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIPT1	NM_145199.3 linkuse as main transcript	c.-2+76G>T		intron_variant		ENST00000651691.1	NP_660200.1	Q9Y234

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
LIPT1	ENST00000651691.1 linkuse as main transcript	c.-2+76G>T	intron_variant		NM_145199.3	ENSP00000498546.1	Q9Y234
ENSG00000273155	ENST00000410042.1 linkuse as main transcript	c.-154+76G>T	intron_variant	2		ENSP00000387111.1
ENSG00000241962	ENST00000424491.5 linkuse as main transcript	n.63+4608G>T	intron_variant	2		ENSP00000390891.1

Frequencies

GnomAD3 genomes

AF:

0.581

AC:

88246

AN:

151974

Hom.:

26494

Cov.:

show subpopulations

Gnomad AFR

AF:

0.433

Gnomad AMI

AF:

0.634

Gnomad AMR

AF:

0.611

Gnomad ASJ

AF:

0.619

Gnomad EAS

AF:

0.878

Gnomad SAS

AF:

0.623

Gnomad FIN

AF:

0.559

Gnomad MID

AF:

0.728

Gnomad NFE

AF:

0.637

Gnomad OTH

AF:

0.630

GnomAD4 exome

AF:

0.626

AC:

183936

AN:

293924

Hom.:

58239

Cov.:

AF XY:

0.630

AC XY:

105344

AN XY:

167160

show subpopulations

Gnomad4 AFR exome

AF:

0.437

Gnomad4 AMR exome

AF:

0.557

Gnomad4 ASJ exome

AF:

0.629

Gnomad4 EAS exome

AF:

0.876

Gnomad4 SAS exome

AF:

0.625

Gnomad4 FIN exome

AF:

0.576

Gnomad4 NFE exome

AF:

0.636

Gnomad4 OTH exome

AF:

0.627

GnomAD4 genome

AF:

0.581

AC:

88290

AN:

152092

Hom.:

26506

Cov.:

AF XY:

0.580

AC XY:

43134

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.433

Gnomad4 AMR

AF:

0.611

Gnomad4 ASJ

AF:

0.619

Gnomad4 EAS

AF:

0.878

Gnomad4 SAS

AF:

0.623

Gnomad4 FIN

AF:

0.559

Gnomad4 NFE

AF:

0.637

Gnomad4 OTH

AF:

0.633

Alfa

AF:

0.596

Hom.:

3405

Bravo

AF:

0.576

Asia WGS

AF:

0.703

AC:

2446

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.2

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over