rs3746806
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_033409.4(SLC52A3):c.705C>T(p.Leu235=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00183 in 1,614,156 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L235L) has been classified as Benign.
Frequency
Consequence
NM_033409.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC52A3 | NM_033409.4 | c.705C>T | p.Leu235= | synonymous_variant | 3/5 | ENST00000645534.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC52A3 | ENST00000645534.1 | c.705C>T | p.Leu235= | synonymous_variant | 3/5 | NM_033409.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00960 AC: 1460AN: 152148Hom.: 15 Cov.: 32
GnomAD3 exomes AF: 0.00273 AC: 687AN: 251366Hom.: 12 AF XY: 0.00199 AC XY: 271AN XY: 135870
GnomAD4 exome AF: 0.00102 AC: 1485AN: 1461890Hom.: 14 Cov.: 63 AF XY: 0.000891 AC XY: 648AN XY: 727244
GnomAD4 genome ? AF: 0.00965 AC: 1470AN: 152266Hom.: 15 Cov.: 32 AF XY: 0.00924 AC XY: 688AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 16, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 21, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 23, 2017 | p.Leu235Leu in exon 3 of SLC52A3: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wit hin the splice consensus sequence, and has been identified in 3.74% (388/10376) of African chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.br oadinstitute.org; dbSNP rs3746806). - |
Brown-Vialetto-van Laere syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at