chr12-1831132-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001039029.3(LRTM2):c.265G>A(p.Ala89Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039029.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRTM2 | NM_001039029.3 | c.265G>A | p.Ala89Thr | missense_variant | 4/5 | ENST00000299194.6 | |
CACNA2D4 | NM_172364.5 | c.2551+9607C>T | intron_variant | ENST00000382722.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRTM2 | ENST00000299194.6 | c.265G>A | p.Ala89Thr | missense_variant | 4/5 | 2 | NM_001039029.3 | P1 | |
CACNA2D4 | ENST00000382722.10 | c.2551+9607C>T | intron_variant | 1 | NM_172364.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 250980Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135716
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461562Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727084
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 03, 2022 | The c.265G>A (p.A89T) alteration is located in exon 4 (coding exon 2) of the LRTM2 gene. This alteration results from a G to A substitution at nucleotide position 265, causing the alanine (A) at amino acid position 89 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