11-557617-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173573.3(LMNTD2):c.579G>A(p.Met193Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 1,613,194 control chromosomes in the GnomAD database, including 1,311 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.
Frequency
Consequence
NM_173573.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMNTD2 | ENST00000329451.8 | c.579G>A | p.Met193Ile | missense_variant | Exon 6 of 14 | 1 | NM_173573.3 | ENSP00000331167.3 | ||
LMNTD2 | ENST00000441853.5 | c.600G>A | p.Met200Ile | missense_variant | Exon 7 of 9 | 3 | ENSP00000393529.1 | |||
LMNTD2 | ENST00000486629.1 | c.609G>A | p.Met203Ile | missense_variant | Exon 6 of 7 | 5 | ENSP00000435529.1 | |||
LMNTD2-AS1 | ENST00000527620.5 | n.23C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0369 AC: 5617AN: 152170Hom.: 108 Cov.: 33
GnomAD3 exomes AF: 0.0371 AC: 9293AN: 250348Hom.: 223 AF XY: 0.0381 AC XY: 5170AN XY: 135618
GnomAD4 exome AF: 0.0383 AC: 56003AN: 1460906Hom.: 1203 Cov.: 36 AF XY: 0.0386 AC XY: 28047AN XY: 726728
GnomAD4 genome AF: 0.0369 AC: 5625AN: 152288Hom.: 108 Cov.: 33 AF XY: 0.0379 AC XY: 2825AN XY: 74476
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at