rs3746807

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_033409.4(SLC52A3):c.456C>T(p.Pro152Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 1,613,980 control chromosomes in the GnomAD database, including 9,579 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 806 hom., cov: 32)

Exomes 𝑓: 0.11 ( 8773 hom. )

Consequence

SLC52A3
NM_033409.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.14

Publications

11 publications found

Variant links:

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 1
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, G2P, ClinGen, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), PanelApp Australia
progressive bulbar palsy
Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

SLC52A3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 20-765319-G-A is Benign according to our data. Variant chr20-765319-G-A is described in ClinVar as Benign. ClinVar VariationId is 262234.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.14 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC52A3	NM_033409.4 link	c.456C>T	p.Pro152Pro	synonymous_variant	Exon 2 of 5	ENST00000645534.1	NP_212134.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC52A3	ENST00000645534.1 link	c.456C>T	p.Pro152Pro	synonymous_variant	Exon 2 of 5		NM_033409.4	ENSP00000494193.1

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15334

AN:

152016

Hom.:

805

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.0837

Gnomad ASJ

AF:

0.0505

Gnomad EAS

AF:

0.179

Gnomad SAS

AF:

0.0527

Gnomad FIN

AF:

0.0983

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.103

Gnomad OTH

AF:

0.0917

GnomAD2 exomes

AF:

0.0957

AC:

24062

AN:

251434

AF XY:

0.0941

show subpopulations

Gnomad AFR exome

AF:

0.105

Gnomad AMR exome

AF:

0.0544

Gnomad ASJ exome

AF:

0.0575

Gnomad EAS exome

AF:

0.177

Gnomad FIN exome

AF:

0.107

Gnomad NFE exome

AF:

0.103

Gnomad OTH exome

AF:

0.0908

GnomAD4 exome

AF:

0.106

AC:

154446

AN:

1461846

Hom.:

8773

Cov.:

AF XY:

0.105

AC XY:

76092

AN XY:

727228

show subpopulations

African (AFR)

AF:

0.101

AC:

3365

AN:

33480

American (AMR)

AF:

0.0566

AC:

2532

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0562

AC:

1468

AN:

26136

East Asian (EAS)

AF:

0.217

AC:

8616

AN:

39700

South Asian (SAS)

AF:

0.0652

AC:

5623

AN:

86258

European-Finnish (FIN)

AF:

0.109

AC:

5821

AN:

53414

Middle Eastern (MID)

AF:

0.0480

AC:

277

AN:

5768

European-Non Finnish (NFE)

AF:

0.109

AC:

120737

AN:

1111970

Other (OTH)

AF:

0.0995

AC:

6007

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

9363

18725

28088

37450

46813

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4430

8860

13290

17720

22150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.101

AC:

15363

AN:

152134

Hom.:

806

Cov.:

AF XY:

0.0998

AC XY:

7425

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.105

AC:

4369

AN:

41494

American (AMR)

AF:

0.0836

AC:

1277

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0505

AC:

175

AN:

3466

East Asian (EAS)

AF:

0.180

AC:

926

AN:

5152

South Asian (SAS)

AF:

0.0521

AC:

251

AN:

4818

European-Finnish (FIN)

AF:

0.0983

AC:

1043

AN:

10614

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.103

AC:

6992

AN:

67988

Other (OTH)

AF:

0.0907

AC:

192

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

687

1373

2060

2746

3433

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.102

Hom.:

3941

Bravo

AF:

0.102

Asia WGS

AF:

0.125

AC:

436

AN:

3478

EpiCase

AF:

0.0961

EpiControl

AF:

0.0962

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Aug 23, 2017

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

p.Pro152Pro in exon 2 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 18.19% (1570/8630) of East Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exa c.broadinstitute.org; dbSNP rs3746807). -

not provided

Benign:2

Jul 03, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Brown-Vialetto-van Laere syndrome 1

Benign:1

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

5.3

(source)

DANN

Benign

0.75

PhyloP100

-1.1

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over