20-761009-CG-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_033409.4(SLC52A3):c.*16del 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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -0.180

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]

ACMG classification

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	UniProt
SLC52A3	NM_033409.4	c.*16del		3_prime_UTR_variant	5/5	ENST00000645534.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC52A3	ENST00000645534.1	c.*16del		3_prime_UTR_variant	5/5		NM_033409.4	P1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17672 AN: 152070 Hom.: 1337 Cov.: 30

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

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.: 28 AF XY: 0.121 AC XY: 85786 AN XY: 711584

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.: 30 AF XY: 0.122 AC XY: 9063 AN XY: 74406

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

Submissions by phenotype

not specified Benign:3

Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
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

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

Other links and lift over

dbSNP: rs3215628; hg19: chr20-741653;