12-25520039-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001145728.2(LMNTD1):c.835G>A(p.Ala279Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000201 in 1,612,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145728.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMNTD1 | NM_001145728.2 | c.835G>A | p.Ala279Thr | missense_variant | 7/10 | ENST00000458174.7 | NP_001139200.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMNTD1 | ENST00000458174.7 | c.835G>A | p.Ala279Thr | missense_variant | 7/10 | 2 | NM_001145728.2 | ENSP00000407353.2 |
Frequencies
GnomAD3 genomes AF: 0.0000463 AC: 7AN: 151314Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251336Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135836
GnomAD4 exome AF: 0.000217 AC: 317AN: 1461548Hom.: 0 Cov.: 31 AF XY: 0.000201 AC XY: 146AN XY: 727080
GnomAD4 genome AF: 0.0000463 AC: 7AN: 151314Hom.: 0 Cov.: 28 AF XY: 0.0000271 AC XY: 2AN XY: 73818
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.835G>A (p.A279T) alteration is located in exon 7 (coding exon 6) of the LMNTD1 gene. This alteration results from a G to A substitution at nucleotide position 835, causing the alanine (A) at amino acid position 279 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