chr18-59333237-T-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005570.4(LMAN1):c.1228A>T(p.Met410Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 1,612,408 control chromosomes in the GnomAD database, including 14,988 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005570.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMAN1 | NM_005570.4 | c.1228A>T | p.Met410Leu | missense_variant | 11/13 | ENST00000251047.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMAN1 | ENST00000251047.6 | c.1228A>T | p.Met410Leu | missense_variant | 11/13 | 1 | NM_005570.4 | P1 | |
LMAN1 | ENST00000587918.1 | n.455A>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.106 AC: 16131AN: 151872Hom.: 1065 Cov.: 32
GnomAD3 exomes AF: 0.121 AC: 30299AN: 250040Hom.: 2077 AF XY: 0.119 AC XY: 16020AN XY: 135114
GnomAD4 exome AF: 0.134 AC: 196412AN: 1460418Hom.: 13924 Cov.: 33 AF XY: 0.133 AC XY: 96280AN XY: 726538
GnomAD4 genome AF: 0.106 AC: 16136AN: 151990Hom.: 1064 Cov.: 32 AF XY: 0.106 AC XY: 7903AN XY: 74294
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Factor V and factor VIII, combined deficiency of, type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at