chr12-25552902-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145728.2(LMNTD1):c.58G>A(p.Glu20Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,552,412 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMNTD1 | NM_001145728.2 | c.58G>A | p.Glu20Lys | missense_variant | 2/10 | ENST00000458174.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMNTD1 | ENST00000458174.7 | c.58G>A | p.Glu20Lys | missense_variant | 2/10 | 2 | NM_001145728.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000559 AC: 85AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000169 AC: 27AN: 159924Hom.: 0 AF XY: 0.000131 AC XY: 11AN XY: 83952
GnomAD4 exome AF: 0.0000614 AC: 86AN: 1400102Hom.: 1 Cov.: 30 AF XY: 0.0000521 AC XY: 36AN XY: 690964
GnomAD4 genome AF: 0.000565 AC: 86AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74478
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at