chr11-557894-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173573.3(LMNTD2):c.545G>A(p.Gly182Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,569,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173573.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMNTD2 | ENST00000329451.8 | c.545G>A | p.Gly182Asp | missense_variant | Exon 5 of 14 | 1 | NM_173573.3 | ENSP00000331167.3 | ||
LMNTD2 | ENST00000441853.5 | c.566G>A | p.Gly189Asp | missense_variant | Exon 6 of 9 | 3 | ENSP00000393529.1 | |||
LMNTD2 | ENST00000486629.1 | c.575G>A | p.Gly192Asp | missense_variant | Exon 5 of 7 | 5 | ENSP00000435529.1 | |||
LMNTD2-AS1 | ENST00000527620.5 | n.300C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000101 AC: 20AN: 197394Hom.: 0 AF XY: 0.0000939 AC XY: 10AN XY: 106476
GnomAD4 exome AF: 0.0000480 AC: 68AN: 1417668Hom.: 0 Cov.: 36 AF XY: 0.0000528 AC XY: 37AN XY: 700982
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.545G>A (p.G182D) alteration is located in exon 5 (coding exon 5) of the LMNTD2 gene. This alteration results from a G to A substitution at nucleotide position 545, causing the glycine (G) at amino acid position 182 to be replaced by an aspartic acid (D). 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