rs17160390
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016579.4(CD320):c.143-769T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,098 control chromosomes in the GnomAD database, including 2,032 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 0.11 ( 2032 hom., cov: 31)
Exomes 𝑓: 0.037 ( 0 hom. )
Consequence
CD320
NM_016579.4 intron
NM_016579.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0660
Genes affected
CD320 (HGNC:16692): (CD320 molecule) This gene encodes the transcobalamin receptor that is expressed at the cell surface. It mediates the cellular uptake of transcobalamin bound cobalamin (vitamin B12), and is involved in B-cell proliferation and immunoglobulin secretion. Mutations in this gene are associated with methylmalonic aciduria. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2011]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD320 | NM_016579.4 | c.143-769T>C | intron_variant | ENST00000301458.10 | |||
CD320 | NM_001165895.2 | c.143-1837T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD320 | ENST00000301458.10 | c.143-769T>C | intron_variant | 1 | NM_016579.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.114 AC: 17334AN: 151900Hom.: 2024 Cov.: 31
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GnomAD4 exome AF: 0.0375 AC: 3AN: 80Hom.: 0 Cov.: 0 AF XY: 0.0385 AC XY: 2AN XY: 52
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GnomAD4 genome ? AF: 0.114 AC: 17365AN: 152018Hom.: 2032 Cov.: 31 AF XY: 0.113 AC XY: 8412AN XY: 74330
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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