Variant rs73576869 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_033409.4(SLC52A3):c.1073+21A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 1,613,696 control chromosomes in the GnomAD database, including 1,161 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 114 hom., cov: 33)

Exomes 𝑓: 0.013 ( 1047 hom. )

Consequence

SLC52A3
NM_033409.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0890

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 20-763477-T-A is Benign according to our data. Variant chr20-763477-T-A is described in ClinVar as [Benign]. Clinvar id is 262229.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 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.1073+21A>T		intron_variant		ENST00000645534.1	NP_212134.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC52A3	ENST00000645534.1 linkuse as main transcript	c.1073+21A>T		intron_variant			NM_033409.4	ENSP00000494193	P1	Q9NQ40-1

Frequencies

GnomAD3 genomes

AF:

0.0182

AC:

2764

AN:

152144

Hom.:

116

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0196

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0128

Gnomad ASJ

AF:

0.00634

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.0219

Gnomad FIN

AF:

0.0317

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00495

Gnomad OTH

AF:

0.0158

GnomAD3 exomes

AF:

0.0244

AC:

6111

AN:

250746

Hom.:

330

AF XY:

0.0235

AC XY:

3184

AN XY:

135582

show subpopulations

Gnomad AFR exome

AF:

0.0194

Gnomad AMR exome

AF:

0.00938

Gnomad ASJ exome

AF:

0.00586

Gnomad EAS exome

AF:

0.173

Gnomad SAS exome

AF:

0.0241

Gnomad FIN exome

AF:

0.0337

Gnomad NFE exome

AF:

0.00590

Gnomad OTH exome

AF:

0.0181

GnomAD4 exome

AF:

0.0128

AC:

18668

AN:

1461434

Hom.:

1047

Cov.:

AF XY:

0.0133

AC XY:

9659

AN XY:

727010

show subpopulations

Gnomad4 AFR exome

AF:

0.0197

Gnomad4 AMR exome

AF:

0.00933

Gnomad4 ASJ exome

AF:

0.00601

Gnomad4 EAS exome

AF:

0.207

Gnomad4 SAS exome

AF:

0.0239

Gnomad4 FIN exome

AF:

0.0319

Gnomad4 NFE exome

AF:

0.00405

Gnomad4 OTH exome

AF:

0.0154

GnomAD4 genome

AF:

0.0181

AC:

2763

AN:

152262

Hom.:

114

Cov.:

AF XY:

0.0208

AC XY:

1546

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.0196

Gnomad4 AMR

AF:

0.0127

Gnomad4 ASJ

AF:

0.00634

Gnomad4 EAS

AF:

0.178

Gnomad4 SAS

AF:

0.0220

Gnomad4 FIN

AF:

0.0317

Gnomad4 NFE

AF:

0.00494

Gnomad4 OTH

AF:

0.0156

Alfa

AF:

0.0114

Hom.:

Bravo

AF:

0.0188

Asia WGS

AF:

0.100

AC:

350

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 27, 2018	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.85

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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