rs6117615

Variant names:

• chr20-778672-A-G
• rs6117615
• XM_047439868.1:c.-238+1340T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-778672-A-G
• chr20-778672-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047439868.1(SLC52A3):​c.-238+1340T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0765 in 151,886 control chromosomes in the GnomAD database, including 763 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 0.076 (763 hom., cov: 32)
• Consequence: SLC52A3 XM_047439868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 5 publications found

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 Gene-Disease associations (from GenCC):

• Brown-Vialetto-van Laere syndrome 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, G2P, ClinGen, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), PanelApp Australia
• progressive bulbar palsy

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC52A3	XM_047439868.1	c.-238+1340T>C		intron_variant	Intron 1 of 5		XP_047295824.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0765 AC: 11613 AN: 151776 Hom.: 763 Cov.: 32

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0490

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.0765 AC: 11615 AN: 151886 Hom.: 763 Cov.: 32 AF XY: 0.0752 AC XY: 5578 AN XY: 74224

African (AFR) AF: 0.0787 AC: 3263 AN: 41442

American (AMR) AF: 0.0488 AC: 745 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2182 AN: 5120

South Asian (SAS) AF: 0.0286 AC: 138 AN: 4820

European-Finnish (FIN) AF: 0.0452 AC: 476 AN: 10522

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0648 AC: 4401 AN: 67948

Other (OTH) AF: 0.0721 AC: 152 AN: 2108

Alfa AF: 0.0733 Hom.: 2569

Bravo AF: 0.0793

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.71
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs6117615; hg19: chr20-759315;