rs10498869
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018368.4(LMBRD1):c.473+2555C>T variant causes a intron change. The variant allele was found at a frequency of 0.0636 in 170,136 control chromosomes in the GnomAD database, including 501 homozygotes. 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 0.063 ( 459 hom., cov: 30)
Exomes 𝑓: 0.064 ( 42 hom. )
Consequence
LMBRD1
NM_018368.4 intron
NM_018368.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.08
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]
GAPDHP42 (HGNC:37799): (glyceraldehyde 3 phosphate dehydrogenase pseudogene 42)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0807 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMBRD1 | NM_018368.4 | c.473+2555C>T | intron_variant | ENST00000649934.3 | |||
LOC124901337 | XR_007059630.1 | n.2552C>T | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMBRD1 | ENST00000649934.3 | c.473+2555C>T | intron_variant | NM_018368.4 | P2 | ||||
GAPDHP42 | ENST00000406848.1 | n.916G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0635 AC: 9653AN: 151968Hom.: 458 Cov.: 30
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GnomAD4 exome AF: 0.0643 AC: 1160AN: 18050Hom.: 42 Cov.: 0 AF XY: 0.0638 AC XY: 681AN XY: 10670
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GnomAD4 genome ? AF: 0.0635 AC: 9655AN: 152086Hom.: 459 Cov.: 30 AF XY: 0.0665 AC XY: 4942AN XY: 74352
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ClinVar
Not reported inComputational 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