chr20-761029-G-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_033409.4(SLC52A3):c.1407C>G(p.Ala469Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000276 in 1,451,410 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
SLC52A3
NM_033409.4 synonymous
NM_033409.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.286
Publications
0 publications found
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]
SLC52A3 Gene-Disease associations (from GenCC):
- 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
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 20-761029-G-C is Benign according to our data. Variant chr20-761029-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1375233.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.286 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1451410Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 721332 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1451410
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
721332
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33176
American (AMR)
AF:
AC:
0
AN:
43744
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25986
East Asian (EAS)
AF:
AC:
0
AN:
38876
South Asian (SAS)
AF:
AC:
0
AN:
84610
European-Finnish (FIN)
AF:
AC:
0
AN:
51274
Middle Eastern (MID)
AF:
AC:
0
AN:
5666
European-Non Finnish (NFE)
AF:
AC:
4
AN:
1108176
Other (OTH)
AF:
AC:
0
AN:
59902
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.463
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Brown-Vialetto-van Laere syndrome 1 Benign:1
Jan 05, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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