12-120694297-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014730.4(MLEC):c.414+28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 1,606,068 control chromosomes in the GnomAD database, including 129,963 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.49 ( 20983 hom., cov: 32)
Exomes 𝑓: 0.38 ( 108980 hom. )
Consequence
MLEC
NM_014730.4 intron
NM_014730.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.107
Genes affected
MLEC (HGNC:28973): (malectin) This gene encodes the carbohydrate-binding protein malectin which is a Type I membrane-anchored endoplasmic reticulum protein. This protein has an affinity for Glc2Man9GlcNAc2 (G2M9) N-glycans and is involved in regulating glycosylation in the endoplasmic reticulum. This protein has also been shown to interact with ribophorin I and may be involved in the directing the degradation of misfolded proteins. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 12-120694297-C-T is Benign according to our data. Variant chr12-120694297-C-T is described in ClinVar as [Benign]. Clinvar id is 1237132.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MLEC | NM_014730.4 | c.414+28C>T | intron_variant | ENST00000228506.8 | NP_055545.1 | |||
MLEC | NM_001303627.2 | c.165+28C>T | intron_variant | NP_001290556.1 | ||||
MLEC | NM_001303628.2 | c.414+28C>T | intron_variant | NP_001290557.1 | ||||
MLEC | XM_011539032.2 | c.165+28C>T | intron_variant | XP_011537334.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MLEC | ENST00000228506.8 | c.414+28C>T | intron_variant | 1 | NM_014730.4 | ENSP00000228506 | P1 | |||
MLEC | ENST00000412616.2 | c.414+28C>T | intron_variant | 3 | ENSP00000440746 | |||||
MLEC | ENST00000535656.1 | c.103+28C>T | intron_variant | 3 | ENSP00000441247 | |||||
MLEC | ENST00000545525.5 | c.165+28C>T | intron_variant | 2 | ENSP00000438950 |
Frequencies
GnomAD3 genomes AF: 0.490 AC: 74495AN: 151904Hom.: 20939 Cov.: 32
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GnomAD3 exomes AF: 0.434 AC: 107215AN: 246814Hom.: 24990 AF XY: 0.425 AC XY: 56671AN XY: 133334
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GnomAD4 exome AF: 0.378 AC: 548989AN: 1454046Hom.: 108980 Cov.: 31 AF XY: 0.379 AC XY: 274269AN XY: 723040
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GnomAD4 genome AF: 0.491 AC: 74596AN: 152022Hom.: 20983 Cov.: 32 AF XY: 0.493 AC XY: 36604AN XY: 74320
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 10, 2019 | This variant is associated with the following publications: (PMID: 28972276) - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at