17-5033011-GC-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_017986.4(SLC52A1):c.1292del(p.Ser431ThrfsTer13) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,516 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
SLC52A1
NM_017986.4 frameshift
NM_017986.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.616
Genes affected
SLC52A1 (HGNC:30225): (solute carrier family 52 member 1) Biological redox reactions require electron donors and acceptor. Vitamin B2 is the source for the flavin in flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) which are common redox reagents. This gene encodes a member of the riboflavin (vitamin B2) transporter family. Haploinsufficiency of this protein can cause maternal riboflavin deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC52A1 | NM_017986.4 | c.1292del | p.Ser431ThrfsTer13 | frameshift_variant | 5/5 | ENST00000254853.10 | |
LOC105371501 | XR_002958101.2 | n.339+1343del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC52A1 | ENST00000254853.10 | c.1292del | p.Ser431ThrfsTer13 | frameshift_variant | 5/5 | 1 | NM_017986.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
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31
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250216Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135214
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GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461516Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727022
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GnomAD4 genome ? Cov.: 31
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Ariboflavinosis Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 22, 2023 | This variant has not been reported in the literature in individuals affected with SLC52A1-related conditions. This variant is present in population databases (rs754376857, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Ser431Thrfs*13) in the SLC52A1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 18 amino acid(s) of the SLC52A1 protein. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
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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