chr8-38392669-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001286819.2(LETM2):c.175C>A(p.Pro59Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000681 in 1,614,096 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001286819.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LETM2 | NM_001286819.2 | c.175C>A | p.Pro59Thr | missense_variant | 3/11 | ENST00000379957.9 | NP_001273748.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LETM2 | ENST00000379957.9 | c.175C>A | p.Pro59Thr | missense_variant | 3/11 | 5 | NM_001286819.2 | ENSP00000369291 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000361 AC: 55AN: 152154Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251422Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135902
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461824Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727206
GnomAD4 genome AF: 0.000361 AC: 55AN: 152272Hom.: 1 Cov.: 32 AF XY: 0.000416 AC XY: 31AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | The c.34C>A (p.P12T) alteration is located in exon 3 (coding exon 1) of the LETM2 gene. This alteration results from a C to A substitution at nucleotide position 34, causing the proline (P) at amino acid position 12 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at