rs3835325
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_005570.4(LMAN1):c.539+11_539+12delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,430,510 control chromosomes in the GnomAD database, including 17,657 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.14 ( 1582 hom., cov: 30)
Exomes 𝑓: 0.15 ( 16075 hom. )
Consequence
LMAN1
NM_005570.4 intron
NM_005570.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.412
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 18-59354506-AAC-A is Benign according to our data. Variant chr18-59354506-AAC-A is described in ClinVar as [Likely_benign]. Clinvar id is 259797.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMAN1 | NM_005570.4 | c.539+11_539+12delGT | intron_variant | ENST00000251047.6 | NP_005561.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.136 AC: 20717AN: 152030Hom.: 1577 Cov.: 30
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GnomAD3 exomes AF: 0.150 AC: 37392AN: 249170Hom.: 3044 AF XY: 0.153 AC XY: 20577AN XY: 134712
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GnomAD4 exome AF: 0.153 AC: 195436AN: 1278364Hom.: 16075 AF XY: 0.154 AC XY: 99568AN XY: 645594
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GnomAD4 genome AF: 0.136 AC: 20723AN: 152146Hom.: 1582 Cov.: 30 AF XY: 0.136 AC XY: 10087AN XY: 74368
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
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
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at