rs910858

chr20-763183-G-Achr20-763183-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_033409.4(SLC52A3):c.1073+315C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,092 control chromosomes in the GnomAD database, including 33,535 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.65 (33535 hom., cov: 34)
• Consequence: SLC52A3 NM_033409.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.478

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 20-763183-G-A is Benign according to our data. Variant chr20-763183-G-A is described in ClinVar as [Benign]. Clinvar id is 1252697.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC52A3	NM_033409.4	c.1073+315C>T		intron_variant		ENST00000645534.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC52A3	ENST00000645534.1	c.1073+315C>T		intron_variant			NM_033409.4	P1

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98512 AN: 151974 Hom.: 33504 Cov.: 34

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.648 AC: 98588 AN: 152092 Hom.: 33535 Cov.: 34 AF XY: 0.651 AC XY: 48365 AN XY: 74326

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.667

Alfa AF: 0.714 Hom.: 48738

Bravo AF: 0.634

Asia WGS AF: 0.762 AC: 2653 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.85
Dann	Benign	0.75

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: rs910858; hg19: chr20-743827;