rs13042395

chr20-773867-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370085.1(SLC52A3):c.-238+2088G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0628 in 152,292 control chromosomes in the GnomAD database, including 705 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.063 (705 hom., cov: 32)
• Consequence: SLC52A3 NM_001370085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC52A3	NM_001370085.1	c.-238+2088G>A		intron_variant
SLC52A3	NM_001370086.1	c.-747+2088G>A		intron_variant
SLC52A3	XM_024451821.1	c.-238+1024G>A		intron_variant
SLC52A3	XM_047439868.1	c.-237-5385G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC52A3	ENST00000217254.11	c.-238+2088G>A		intron_variant		5		P1
SLC52A3	ENST00000674666.1	c.-747+2088G>A		intron_variant
SLC52A3	ENST00000676154.1	c.-52+2088G>A		intron_variant
SLC52A3	ENST00000675466.1	n.29+2088G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0629 AC: 9571 AN: 152174 Hom.: 708 Cov.: 32

Gnomad AFR AF: 0.0155

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.0312

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.0698

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0628 AC: 9557 AN: 152292 Hom.: 705 Cov.: 32 AF XY: 0.0623 AC XY: 4637 AN XY: 74468

Gnomad4 AFR AF: 0.0154

Gnomad4 AMR AF: 0.0476

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.0306

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0718

Gnomad4 OTH AF: 0.0695

Alfa AF: 0.0658 Hom.: 195

Bravo AF: 0.0640

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.8
Dann	Benign	0.50

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: rs13042395; hg19: chr20-754511;