Variant chr20-761009-CG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_033409.4(SLC52A3):c.*16delC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,586,672 control chromosomes in the GnomAD database, including 14,079 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1343 hom., cov: 30)

Exomes 𝑓: 0.12 ( 12736 hom. )

Consequence

SLC52A3
NM_033409.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.180

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 -16 ACMG points.

BP6

Variant 20-761009-CG-C is Benign according to our data. Variant chr20-761009-CG-C is described in ClinVar as [Benign]. Clinvar id is 262227.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-761009-CG-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 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.*16delC		3_prime_UTR_variant	5/5	ENST00000645534.1	NP_212134.3	Q9NQ40-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC52A3	ENST00000645534 linkuse as main transcript	c.*16delC		3_prime_UTR_variant	5/5		NM_033409.4	ENSP00000494193.1		Q9NQ40-1

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17672

AN:

152070

Hom.:

1337

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0665

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.133

Gnomad EAS

AF:

0.368

Gnomad SAS

AF:

0.167

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.127

GnomAD3 exomes

AF:

0.149

AC:

29852

AN:

199770

Hom.:

2754

AF XY:

0.146

AC XY:

16012

AN XY:

109762

show subpopulations

Gnomad AFR exome

AF:

0.0664

Gnomad AMR exome

AF:

0.207

Gnomad ASJ exome

AF:

0.131

Gnomad EAS exome

AF:

0.349

Gnomad SAS exome

AF:

0.166

Gnomad FIN exome

AF:

0.136

Gnomad NFE exome

AF:

0.107

Gnomad OTH exome

AF:

0.139

GnomAD4 exome

AF:

0.120

AC:

171486

AN:

1434484

Hom.:

12736

Cov.:

AF XY:

0.121

AC XY:

85786

AN XY:

711584

show subpopulations

Gnomad4 AFR exome

AF:

0.0657

Gnomad4 AMR exome

AF:

0.204

Gnomad4 ASJ exome

AF:

0.132

Gnomad4 EAS exome

AF:

0.421

Gnomad4 SAS exome

AF:

0.163

Gnomad4 FIN exome

AF:

0.131

Gnomad4 NFE exome

AF:

0.104

Gnomad4 OTH exome

AF:

0.122

GnomAD4 genome

AF:

0.116

AC:

17693

AN:

152188

Hom.:

1343

Cov.:

AF XY:

0.122

AC XY:

9063

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0670

Gnomad4 AMR

AF:

0.179

Gnomad4 ASJ

AF:

0.133

Gnomad4 EAS

AF:

0.368

Gnomad4 SAS

AF:

0.168

Gnomad4 FIN

AF:

0.129

Gnomad4 NFE

AF:

0.106

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.113

Hom.:

190

Bravo

AF:

0.117

Asia WGS

AF:

0.255

AC:

883

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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