rs3833341

Variant names:

• chr20-764018-A-ACAGGTCAAT
• rs3833341
• NM_033409.4:c.568-16_568-15insATTGACCTG

Your query was ambiguous. Multiple possible variants found:

• chr20-764018-A-ACAGGTCAAT
• chr20-764018-A-ACAGGT
• chr20-764018-A-ACAGGTCAGT
• chr20-764018-A-ACAGGTCGAT

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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 -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033409.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC52A3	NM_033409.4	MANE Select	c.568-16_568-15insATTGACCTG		intron	N/A	NP_212134.3
	SLC52A3	NM_001370085.1		c.568-16_568-15insATTGACCTG		intron	N/A	NP_001357014.1	Q9NQ40-1
	SLC52A3	NM_001370086.1		c.568-16_568-15insATTGACCTG		intron	N/A	NP_001357015.1	Q9NQ40-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC52A3	ENST00000645534.1	MANE Select	c.568-16_568-15insATTGACCTG		intron	N/A	ENSP00000494193.1	Q9NQ40-1
	SLC52A3	ENST00000217254.11	TSL:5	c.568-16_568-15insATTGACCTG		intron	N/A	ENSP00000217254.7	Q9NQ40-1
	SLC52A3	ENST00000488495.3	TSL:3	c.568-16_568-15insATTGACCTG		intron	N/A	ENSP00000494009.1	Q9NQ40-1

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

African (AFR) AF: 0.466 AC: 14730 AN: 31622

American (AMR) AF: 0.352 AC: 12656 AN: 35928

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 15161 AN: 25068

East Asian (EAS) AF: 0.572 AC: 20506 AN: 35880

South Asian (SAS) AF: 0.495 AC: 39546 AN: 79890

European-Finnish (FIN) AF: 0.528 AC: 26291 AN: 49748

Middle Eastern (MID) AF: 0.592 AC: 3015 AN: 5090

European-Non Finnish (NFE) AF: 0.585 AC: 629691 AN: 1075598

Other (OTH) AF: 0.579 AC: 33486 AN: 57878

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

African (AFR) AF: 0.470 AC: 19402 AN: 41300

American (AMR) AF: 0.428 AC: 6527 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2115 AN: 3460

East Asian (EAS) AF: 0.591 AC: 3021 AN: 5112

South Asian (SAS) AF: 0.512 AC: 2459 AN: 4802

European-Finnish (FIN) AF: 0.527 AC: 5547 AN: 10532

Middle Eastern (MID) AF: 0.549 AC: 158 AN: 288

European-Non Finnish (NFE) AF: 0.583 AC: 39449 AN: 67672

Other (OTH) AF: 0.548 AC: 1151 AN: 2102

Alfa AF: 0.558 Hom.: 3985

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	4	not specified (4)
1	-	1	Brown-Vialetto-van Laere syndrome 1 (2)
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3833341; hg19: chr20-744662; COSMIC: COSV54076640;