2-43886424-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_133259.4(LRPPRC):c.*2176A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0179 in 152,330 control chromosomes in the GnomAD database, including 91 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.018 ( 91 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
LRPPRC
NM_133259.4 3_prime_UTR
NM_133259.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.485
Genes affected
LRPPRC (HGNC:15714): (leucine rich pentatricopeptide repeat containing) This gene encodes a leucine-rich protein that has multiple pentatricopeptide repeats (PPR). The precise role of this protein is unknown but studies suggest it may play a role in cytoskeletal organization, vesicular transport, or in transcriptional regulation of both nuclear and mitochondrial genes. The protein localizes primarily to mitochondria and is predicted to have an N-terminal mitochondrial targeting sequence. Mutations in this gene are associated with the French-Canadian type of Leigh syndrome. [provided by RefSeq, Mar 2012]
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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=-0.79).
BP6
?
Variant 2-43886424-T-A is Benign according to our data. Variant chr2-43886424-T-A is described in ClinVar as [Benign]. Clinvar id is 336100.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0611 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRPPRC | NM_133259.4 | c.*2176A>T | 3_prime_UTR_variant | 38/38 | ENST00000260665.12 | ||
LRPPRC | XM_006711915.3 | c.*2176A>T | 3_prime_UTR_variant | 38/38 | |||
LRPPRC | XM_047442809.1 | c.*2176A>T | 3_prime_UTR_variant | 38/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRPPRC | ENST00000260665.12 | c.*2176A>T | 3_prime_UTR_variant | 38/38 | 1 | NM_133259.4 | P3 | ||
LRPPRC | ENST00000684454.1 | n.10225A>T | non_coding_transcript_exon_variant | 7/7 | |||||
LRPPRC | ENST00000682612.1 | c.*2328A>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 |
Frequencies
GnomAD3 genomes ? AF: 0.0179 AC: 2727AN: 152212Hom.: 91 Cov.: 32
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GnomAD4 genome ? AF: 0.0179 AC: 2728AN: 152330Hom.: 91 Cov.: 32 AF XY: 0.0166 AC XY: 1240AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital lactic acidosis, Saguenay-Lac-Saint-Jean type Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at