8-38394218-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001286819.2(LETM2):c.622A>C(p.Thr208Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000194 in 1,491,034 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T208A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001286819.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LETM2 | NM_001286819.2 | c.622A>C | p.Thr208Pro | missense_variant | 4/11 | ENST00000379957.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LETM2 | ENST00000379957.9 | c.622A>C | p.Thr208Pro | missense_variant | 4/11 | 5 | NM_001286819.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000190 AC: 2AN: 105322Hom.: 0 AF XY: 0.0000172 AC XY: 1AN XY: 58202
GnomAD4 exome AF: 0.0000179 AC: 24AN: 1338744Hom.: 0 Cov.: 26 AF XY: 0.0000197 AC XY: 13AN XY: 660188
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.481A>C (p.T161P) alteration is located in exon 4 (coding exon 2) of the LETM2 gene. This alteration results from a A to C substitution at nucleotide position 481, causing the threonine (T) at amino acid position 161 to be replaced by a proline (P). 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