chr20-764018-A-ACAGGTCAAT

Position:

• chr20-764018-A-ACAGGTCAAT

Variant summary

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

The NM_033409.4(SLC52A3):​c.568-16_568-15insATTGACCTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 1,548,112 control chromosomes in the GnomAD database, including 250,805 homozygotes. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.53 (21644 hom., cov: 0)
  • Exomes 𝑓: 0.57 (229161 hom.)
• Consequence: SLC52A3 NM_033409.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts P:1 B:6
• Conservation: PhyloP100: 0.279

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 20-764018-A-ACAGGTCAAT is Benign according to our data. Variant chr20-764018-A-ACAGGTCAAT is described in ClinVar as [Benign]. Clinvar id is 262235.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC52A3	NM_033409.4	c.568-16_568-15insATTGACCTG		intron_variant		ENST00000645534.1	NP_212134.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC52A3	ENST00000645534.1	c.568-16_568-15insATTGACCTG		intron_variant			NM_033409.4	ENSP00000494193.1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80258 AN: 151294 Hom.: 21633 Cov.: 0

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.555

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.550

GnomAD4 exome AF: 0.569 AC: 795082 AN: 1396702 Hom.: 229161 Cov.: 45 AF XY: 0.567 AC XY: 390260 AN XY: 688012

Gnomad4 AFR exome AF: 0.466

Gnomad4 AMR exome AF: 0.352

Gnomad4 ASJ exome AF: 0.605

Gnomad4 EAS exome AF: 0.572

Gnomad4 SAS exome AF: 0.495

Gnomad4 FIN exome AF: 0.528

Gnomad4 NFE exome AF: 0.585

Gnomad4 OTH exome AF: 0.579

GnomAD4 genome AF: 0.530 AC: 80300 AN: 151410 Hom.: 21644 Cov.: 0 AF XY: 0.524 AC XY: 38780 AN XY: 73980

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.548

Alfa AF: 0.558 Hom.: 3985

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1 Benign:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:4

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	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Brown-Vialetto-van Laere syndrome 1 Pathogenic:1 Benign:1

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Pathogenic, no assertion criteria provided	literature only	GeneReviews	Mar 17, 2015	- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3833341; hg19: chr20-744662;