4-1815778-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_012318.3(LETM1):c.1956G>A(p.Glu652Glu) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000372 in 1,614,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
LETM1
NM_012318.3 synonymous
NM_012318.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.64
Genes affected
LETM1 (HGNC:6556): (leucine zipper and EF-hand containing transmembrane protein 1) This gene encodes a protein that is localized to the inner mitochondrial membrane. The protein functions to maintain the mitochondrial tubular shapes and is required for normal mitochondrial morphology and cellular viability. Mutations in this gene cause Wolf-Hirschhorn syndrome, a complex malformation syndrome caused by the deletion of parts of the distal short arm of chromosome 4. Related pseudogenes have been identified on chromosomes 8, 15 and 19. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 4-1815778-C-T is Benign according to our data. Variant chr4-1815778-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1663127.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LETM1 | NM_012318.3 | c.1956G>A | p.Glu652Glu | synonymous_variant | Exon 13 of 14 | ENST00000302787.3 | NP_036450.1 | |
LETM1 | XM_006713884.2 | c.1953G>A | p.Glu651Glu | synonymous_variant | Exon 13 of 14 | XP_006713947.1 | ||
LETM1 | XM_047415673.1 | c.1413G>A | p.Glu471Glu | synonymous_variant | Exon 12 of 13 | XP_047271629.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 34
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461794Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727214
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152364Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74500
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Nov 05, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at