rs73576869
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_033409.4(SLC52A3):c.1073+21A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 1,613,696 control chromosomes in the GnomAD database, including 1,161 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.018 ( 114 hom., cov: 33)
Exomes 𝑓: 0.013 ( 1047 hom. )
Consequence
SLC52A3
NM_033409.4 intron
NM_033409.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0890
Genes affected
SLC52A3 (HGNC:16187): (solute carrier family 52 member 3) This gene encodes a riboflavin transporter protein that is strongly expressed in the intestine and likely plays a role in intestinal absorption of riboflavin. The protein is predicted to have eleven transmembrane domains and a cell surface localization signal in the C-terminus. Mutations at this locus have been associated with Brown-Vialetto-Van Laere syndrome and Fazio-Londe disease. [provided by RefSeq, Mar 2012]
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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=-0.82).
BP6
Variant 20-763477-T-A is Benign according to our data. Variant chr20-763477-T-A is described in ClinVar as [Benign]. Clinvar id is 262229.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC52A3 | NM_033409.4 | c.1073+21A>T | intron_variant | ENST00000645534.1 | NP_212134.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC52A3 | ENST00000645534.1 | c.1073+21A>T | intron_variant | NM_033409.4 | ENSP00000494193 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0182 AC: 2764AN: 152144Hom.: 116 Cov.: 33
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GnomAD3 exomes AF: 0.0244 AC: 6111AN: 250746Hom.: 330 AF XY: 0.0235 AC XY: 3184AN XY: 135582
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GnomAD4 exome AF: 0.0128 AC: 18668AN: 1461434Hom.: 1047 Cov.: 32 AF XY: 0.0133 AC XY: 9659AN XY: 727010
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GnomAD4 genome AF: 0.0181 AC: 2763AN: 152262Hom.: 114 Cov.: 33 AF XY: 0.0208 AC XY: 1546AN XY: 74438
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 27, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at