XM_047439868.1:c.-238+1340T>C

Variant names:

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

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: ClinGen, Ambry Genetics, PanelApp Australia, Genomics England PanelApp, G2P, Labcorp Genetics (formerly Invitae)
• 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;