Genetic Variant SLC52A3:c.-14_-6delGGGCAGATA (chr20-765779-GTATCTGCCC-G) – ACMG Classification: Benign (-16 pts)

Variant summary

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

The NM_033409.4(SLC52A3):c.-14_-6delGGGCAGATA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 1,608,422 control chromosomes in the GnomAD database, including 58,254 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 5977 hom., cov: 18)

Exomes 𝑓: 0.26 ( 52277 hom. )

Consequence

SLC52A3
NM_033409.4 5_prime_UTR

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 1.13

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 20-765779-GTATCTGCCC-G is Benign according to our data. Variant chr20-765779-GTATCTGCCC-G is described in ClinVar as [Benign]. Clinvar id is 262228.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-765779-GTATCTGCCC-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC52A3	NM_033409.4 link	c.-14_-6delGGGCAGATA		5_prime_UTR_variant	Exon 2 of 5	ENST00000645534.1	NP_212134.3	Q9NQ40-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC52A3	ENST00000645534.1 link	c.-14_-6delGGGCAGATA		5_prime_UTR_variant	Exon 2 of 5		NM_033409.4	ENSP00000494193.1		Q9NQ40-1

Frequencies

GnomAD3 genomes

AF:

0.276

AC:

41865

AN:

151712

Hom.:

5976

Cov.:

show subpopulations

Gnomad AFR

AF:

0.340

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.210

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.245

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.270

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.254

GnomAD3 exomes

AF:

0.221

AC:

51450

AN:

232958

Hom.:

6367

AF XY:

0.217

AC XY:

27439

AN XY:

126380

show subpopulations

Gnomad AFR exome

AF:

0.330

Gnomad AMR exome

AF:

0.134

Gnomad ASJ exome

AF:

0.155

Gnomad EAS exome

AF:

0.228

Gnomad SAS exome

AF:

0.101

Gnomad FIN exome

AF:

0.260

Gnomad NFE exome

AF:

0.263

Gnomad OTH exome

AF:

0.230

GnomAD4 exome

AF:

0.263

AC:

383449

AN:

1456592

Hom.:

52277

AF XY:

0.259

AC XY:

187604

AN XY:

724162

show subpopulations

Gnomad4 AFR exome

AF:

0.340

Gnomad4 AMR exome

AF:

0.147

Gnomad4 ASJ exome

AF:

0.170

Gnomad4 EAS exome

AF:

0.312

Gnomad4 SAS exome

AF:

0.116

Gnomad4 FIN exome

AF:

0.273

Gnomad4 NFE exome

AF:

0.278

Gnomad4 OTH exome

AF:

0.255

GnomAD4 genome

AF:

0.276

AC:

41901

AN:

151830

Hom.:

5977

Cov.:

AF XY:

0.270

AC XY:

20061

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.340

Gnomad4 AMR

AF:

0.210

Gnomad4 ASJ

AF:

0.163

Gnomad4 EAS

AF:

0.246

Gnomad4 SAS

AF:

0.109

Gnomad4 FIN

AF:

0.270

Gnomad4 NFE

AF:

0.274

Gnomad4 OTH

AF:

0.254

Alfa

AF:

0.266

Hom.:

978

Bravo

AF:

0.278

Asia WGS

AF:

0.201

AC:

700

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Sep 25, 2017

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

c.-14_-6del in exon 2 of SLC52A3: This variant is not expected to have clinical significance because it has been identified in 33.2% (7594/22860) of African chr omosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitut e.org/; dbSNP rs11467076). -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Jul 03, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Brown-Vialetto-van Laere syndrome 1

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Progressive bulbar palsy of childhood

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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