chr18-59342224-C-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_005570.4(LMAN1):c.956-3271G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 30)
Failed GnomAD Quality Control
Consequence
LMAN1
NM_005570.4 intron
NM_005570.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.627
Publications
5 publications found
Genes affected
LMAN1 (HGNC:6631): (lectin, mannose binding 1) The protein encoded by this gene is a membrane mannose-specific lectin that cycles between the endoplasmic reticulum, endoplasmic reticulum-Golgi intermediate compartment, and cis-Golgi, functioning as a cargo receptor for glycoprotein transport. The protein has an N-terminal signal sequence, a calcium-dependent and pH-sensitive carbohydrate recognition domain, a stalk region that functions in oligomerization, a transmembrane domain, and a short cytoplasmic domain required for organelle targeting. Allelic variants of this gene are associated with the autosomal recessive disorder combined factor V-factor VIII deficiency. [provided by RefSeq, Jul 2015]
LMAN1 Gene-Disease associations (from GenCC):
- factor V and factor VIII, combined deficiency of, type 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, ClinGen, Labcorp Genetics (formerly Invitae)
- combined deficiency of factor V and factor VIIIInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMAN1 | NM_005570.4 | c.956-3271G>T | intron_variant | Intron 8 of 12 | ENST00000251047.6 | NP_005561.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 151804Hom.: 0 Cov.: 30
GnomAD3 genomes
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151804
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151804Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74122
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
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0
AN:
151804
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Cov.:
30
AF XY:
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AN XY:
74122
African (AFR)
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0
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41362
American (AMR)
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0
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15248
Ashkenazi Jewish (ASJ)
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0
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3468
East Asian (EAS)
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0
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5170
South Asian (SAS)
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0
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4808
European-Finnish (FIN)
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0
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10530
Middle Eastern (MID)
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0
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316
European-Non Finnish (NFE)
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0
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67898
Other (OTH)
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0
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2094
Alfa
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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