chr12-1834689-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001039029.3(LRTM2):āc.1081G>Cā(p.Glu361Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,601,732 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.1081G>C | p.Glu361Gln | missense_variant | 5/5 | ENST00000299194.6 | |
CACNA2D4 | NM_172364.5 | c.2551+6050C>G | intron_variant | ENST00000382722.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRTM2 | ENST00000299194.6 | c.1081G>C | p.Glu361Gln | missense_variant | 5/5 | 2 | NM_001039029.3 | P1 | |
CACNA2D4 | ENST00000382722.10 | c.2551+6050C>G | intron_variant | 1 | NM_172364.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000376 AC: 9AN: 239658Hom.: 0 AF XY: 0.0000382 AC XY: 5AN XY: 131020
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1449566Hom.: 0 Cov.: 31 AF XY: 0.0000125 AC XY: 9AN XY: 721284
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 27, 2022 | The c.1081G>C (p.E361Q) alteration is located in exon 5 (coding exon 3) of the LRTM2 gene. This alteration results from a G to C substitution at nucleotide position 1081, causing the glutamic acid (E) at amino acid position 361 to be replaced by a glutamine (Q). 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