chr12-1831063-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.196G>A(p.Val66Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000836 in 1,614,024 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
Genome browser will be placed here
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.196G>A | p.Val66Met | missense_variant | 4/5 | ENST00000299194.6 | |
CACNA2D4 | NM_172364.5 | c.2551+9676C>T | intron_variant | ENST00000382722.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRTM2 | ENST00000299194.6 | c.196G>A | p.Val66Met | missense_variant | 4/5 | 2 | NM_001039029.3 | P1 | |
CACNA2D4 | ENST00000382722.10 | c.2551+9676C>T | intron_variant | 1 | NM_172364.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000836 AC: 21AN: 251248Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135824
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461714Hom.: 0 Cov.: 31 AF XY: 0.0000866 AC XY: 63AN XY: 727178
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2023 | The c.196G>A (p.V66M) 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 196, causing the valine (V) at amino acid position 66 to be replaced by a methionine (M). 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