20-765412-G-C
Variant summary
Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_033409.4(SLC52A3):c.363C>G(p.Thr121Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,613,888 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_033409.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- Brown-Vialetto-van Laere syndrome 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, G2P, ClinGen, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), PanelApp Australia
- progressive bulbar palsyInheritance: AR Classification: MODERATE Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Benign. The variant received -17 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152186Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000315 AC: 79AN: 250504 AF XY: 0.000214 show subpopulations
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461702Hom.: 1 Cov.: 33 AF XY: 0.0000468 AC XY: 34AN XY: 727132 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74340 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:1
p.Thr121Thr in exon 2 of SLC52A3: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 0.29% (32/10982) of Latino chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.br oadinstitute.org; dbSNP rs749966154). -
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Brown-Vialetto-van Laere syndrome 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at