rs34383175
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001363118.2(SLC52A2):c.*19C>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 0.0303 in 1,605,296 control chromosomes in the GnomAD database, including 871 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.024 ( 67 hom., cov: 33)
Exomes 𝑓: 0.031 ( 804 hom. )
Consequence
SLC52A2
NM_001363118.2 3_prime_UTR
NM_001363118.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.524
Genes affected
SLC52A2 (HGNC:30224): (solute carrier family 52 member 2) This gene encodes a membrane protein which belongs to the riboflavin transporter family. In humans, riboflavin must be obtained by intestinal absorption because it cannot be synthesized by the body. The water-soluble vitamin riboflavin is processed to the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which then act as intermediaries in many cellular metabolic reactions. Paralogous members of the riboflavin transporter gene family are located on chromosomes 17 and 20. Unlike other members of this family, this gene has higher expression in brain tissue than small intestine. Alternative splicing of this gene results in multiple transcript variants encoding the same protein. Mutations in this gene have been associated with Brown-Vialetto-Van Laere syndrome 2 - an autosomal recessive progressive neurologic disorder characterized by deafness, bulbar dysfunction, and axial and limb hypotonia. [provided by RefSeq, Jul 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=-0.88).
BP6
Variant 8-144361034-C-T is Benign according to our data. Variant chr8-144361034-C-T is described in ClinVar as [Benign]. Clinvar id is 257671.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144361034-C-T is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0238 (3617/152170) while in subpopulation NFE AF= 0.0367 (2498/67978). AF 95% confidence interval is 0.0355. There are 67 homozygotes in gnomad4. There are 1677 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 67 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC52A2 | NM_001363118.2 | c.*19C>T | 3_prime_UTR_variant | 5/5 | ENST00000643944.2 | NP_001350047.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC52A2 | ENST00000643944.2 | c.*19C>T | 3_prime_UTR_variant | 5/5 | NM_001363118.2 | ENSP00000496184.2 |
Frequencies
GnomAD3 genomes AF: 0.0238 AC: 3617AN: 152052Hom.: 67 Cov.: 33
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GnomAD3 exomes AF: 0.0239 AC: 5960AN: 248976Hom.: 95 AF XY: 0.0238 AC XY: 3203AN XY: 134732
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GnomAD4 exome AF: 0.0310 AC: 45096AN: 1453126Hom.: 804 Cov.: 33 AF XY: 0.0303 AC XY: 21828AN XY: 721484
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GnomAD4 genome AF: 0.0238 AC: 3617AN: 152170Hom.: 67 Cov.: 33 AF XY: 0.0225 AC XY: 1677AN XY: 74390
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 31, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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