Variant chr2-99155070-C-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+19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 455,270 control chromosomes in the GnomAD database, including 86,043 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 26500 hom., cov: 33)

Exomes 𝑓: 0.62 ( 59543 hom. )

Consequence

LIPT1
NM_145199.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0210

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 2-99155070-C-T is Benign according to our data. Variant chr2-99155070-C-T is described in ClinVar as [Benign]. Clinvar id is 379989.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+19C>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+19C>T	intron_variant		NM_145199.3	ENSP00000498546.1	Q9Y234
ENSG00000273155	ENST00000410042.1 linkuse as main transcript	c.-154+19C>T	intron_variant	2		ENSP00000387111.1
ENSG00000241962	ENST00000424491.5 linkuse as main transcript	n.63+4551C>T	intron_variant	2		ENSP00000390891.1

Frequencies

GnomAD3 genomes

AF:

0.580

AC:

88247

AN:

152028

Hom.:

26488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.433

Gnomad AMI

AF:

0.635

Gnomad AMR

AF:

0.611

Gnomad ASJ

AF:

0.619

Gnomad EAS

AF:

0.878

Gnomad SAS

AF:

0.623

Gnomad FIN

AF:

0.558

Gnomad MID

AF:

0.728

Gnomad NFE

AF:

0.636

Gnomad OTH

AF:

0.630

GnomAD3 exomes

AF:

0.625

AC:

80740

AN:

129226

Hom.:

25802

AF XY:

0.632

AC XY:

44613

AN XY:

70594

show subpopulations

Gnomad AFR exome

AF:

0.425

Gnomad AMR exome

AF:

0.552

Gnomad ASJ exome

AF:

0.633

Gnomad EAS exome

AF:

0.872

Gnomad SAS exome

AF:

0.626

Gnomad FIN exome

AF:

0.578

Gnomad NFE exome

AF:

0.637

Gnomad OTH exome

AF:

0.620

GnomAD4 exome

AF:

0.623

AC:

188845

AN:

303124

Hom.:

59543

Cov.:

AF XY:

0.627

AC XY:

108233

AN XY:

172620

show subpopulations

Gnomad4 AFR exome

AF:

0.435

Gnomad4 AMR exome

AF:

0.552

Gnomad4 ASJ exome

AF:

0.626

Gnomad4 EAS exome

AF:

0.876

Gnomad4 SAS exome

AF:

0.624

Gnomad4 FIN exome

AF:

0.576

Gnomad4 NFE exome

AF:

0.633

Gnomad4 OTH exome

AF:

0.622

GnomAD4 genome

AF:

0.580

AC:

88291

AN:

152146

Hom.:

26500

Cov.:

AF XY:

0.580

AC XY:

43137

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.432

Gnomad4 AMR

AF:

0.611

Gnomad4 ASJ

AF:

0.619

Gnomad4 EAS

AF:

0.878

Gnomad4 SAS

AF:

0.623

Gnomad4 FIN

AF:

0.558

Gnomad4 NFE

AF:

0.637

Gnomad4 OTH

AF:

0.633

Alfa

AF:

0.609

Hom.:

5209

Bravo

AF:

0.576

Asia WGS

AF:

0.703

AC:

2445

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 02, 2015

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

8.2

DANN

Benign

0.90

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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