6-69675817-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018368.4(LMBRD1):c.*341C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 269,806 control chromosomes in the GnomAD database, including 42,775 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.57 ( 25110 hom., cov: 32)
Exomes 𝑓: 0.54 ( 17665 hom. )
Consequence
LMBRD1
NM_018368.4 3_prime_UTR
NM_018368.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.23
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 6-69675817-G-A is Benign according to our data. Variant chr6-69675817-G-A is described in ClinVar as [Benign]. Clinvar id is 357765.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMBRD1 | NM_018368.4 | c.*341C>T | 3_prime_UTR_variant | 16/16 | ENST00000649934.3 | NP_060838.3 | ||
LMBRD1 | NM_001363722.2 | c.*341C>T | 3_prime_UTR_variant | 16/16 | NP_001350651.1 | |||
LMBRD1 | NM_001367271.1 | c.*341C>T | 3_prime_UTR_variant | 16/16 | NP_001354200.1 | |||
LMBRD1 | NM_001367272.1 | c.*341C>T | 3_prime_UTR_variant | 16/16 | NP_001354201.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMBRD1 | ENST00000649934.3 | c.*341C>T | 3_prime_UTR_variant | 16/16 | NM_018368.4 | ENSP00000497690 | P2 |
Frequencies
GnomAD3 genomes AF: 0.570 AC: 86450AN: 151798Hom.: 25080 Cov.: 32
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GnomAD4 exome AF: 0.540 AC: 63670AN: 117890Hom.: 17665 Cov.: 0 AF XY: 0.547 AC XY: 34631AN XY: 63306
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GnomAD4 genome AF: 0.570 AC: 86522AN: 151916Hom.: 25110 Cov.: 32 AF XY: 0.571 AC XY: 42405AN XY: 74226
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Methylmalonic aciduria and homocystinuria type cblF 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. - |
Computational scores
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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