rs3214021
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018368.4(LMBRD1):c.1509+22G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 1,599,476 control chromosomes in the GnomAD database, including 129,440 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.36 ( 10557 hom., cov: 31)
Exomes 𝑓: 0.40 ( 118883 hom. )
Consequence
LMBRD1
NM_018368.4 intron
NM_018368.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0240
Genes affected
LMBRD1 (HGNC:23038): (LMBR1 domain containing 1) This gene encodes a lysosomal membrane protein that may be involved in the transport and metabolism of cobalamin. This protein also interacts with the large form of the hepatitis delta antigen and may be required for the nucleocytoplasmic shuttling of the hepatitis delta virus. Mutations in this gene are associated with the vitamin B12 metabolism disorder termed, homocystinuria-megaloblastic anemia complementation type F.[provided by RefSeq, Oct 2009]
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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=-0.87).
BP6
?
Variant 6-69676428-C-T is Benign according to our data. Variant chr6-69676428-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 261024.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMBRD1 | NM_018368.4 | c.1509+22G>A | intron_variant | ENST00000649934.3 | |||
LMBRD1 | NM_001363722.2 | c.1290+22G>A | intron_variant | ||||
LMBRD1 | NM_001367271.1 | c.1290+22G>A | intron_variant | ||||
LMBRD1 | NM_001367272.1 | c.1290+22G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMBRD1 | ENST00000649934.3 | c.1509+22G>A | intron_variant | NM_018368.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.363 AC: 55037AN: 151798Hom.: 10549 Cov.: 31
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GnomAD3 exomes AF: 0.403 AC: 100647AN: 249472Hom.: 20940 AF XY: 0.410 AC XY: 55235AN XY: 134874
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GnomAD4 exome AF: 0.403 AC: 582655AN: 1447558Hom.: 118883 Cov.: 29 AF XY: 0.405 AC XY: 292179AN XY: 721092
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GnomAD4 genome ? AF: 0.362 AC: 55066AN: 151918Hom.: 10557 Cov.: 31 AF XY: 0.361 AC XY: 26819AN XY: 74228
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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:2
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 10, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Methylmalonic aciduria and homocystinuria type cblF Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at