Variant rs3746807 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id is 262234.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-765319-G-A is described in Lovd as [Benign].

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/exons	MANE	Protein	UniProt
SLC52A3	NM_033409.4 linkuse as main transcript	c.456C>T	p.Pro152Pro	synonymous_variant	2/5	ENST00000645534.1	NP_212134.3	Q9NQ40-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC52A3	ENST00000645534.1 linkuse as main transcript	c.456C>T	p.Pro152Pro	synonymous_variant	2/5		NM_033409.4	ENSP00000494193.1		Q9NQ40-1

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

GnomAD3 exomes

AF:

0.0957

AC:

24062

AN:

251434

Hom.:

1344

AF XY:

0.0941

AC XY:

12794

AN XY:

135910

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 SAS exome

AF:

0.0655

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

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.0566

Gnomad4 ASJ exome

AF:

0.0562

Gnomad4 EAS exome

AF:

0.217

Gnomad4 SAS exome

AF:

0.0652

Gnomad4 FIN exome

AF:

0.109

Gnomad4 NFE exome

AF:

0.109

Gnomad4 OTH exome

AF:

0.0995

GnomAD4 genome

AF:

0.101

AC:

15363

AN:

152134

Hom.:

806

Cov.:

AF XY:

0.0998

AC XY:

7425

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.105

Gnomad4 AMR

AF:

0.0836

Gnomad4 ASJ

AF:

0.0505

Gnomad4 EAS

AF:

0.180

Gnomad4 SAS

AF:

0.0521

Gnomad4 FIN

AF:

0.0983

Gnomad4 NFE

AF:

0.103

Gnomad4 OTH

AF:

0.0907

Alfa

AF:

0.0992

Hom.:

1854

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

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Aug 23, 2017	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). -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 03, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Brown-Vialetto-van Laere syndrome 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

5.3

DANN

Benign

0.75

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over