Variant 17-5032883-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000254853.10(SLC52A1):c.*74T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0955 in 1,391,598 control chromosomes in the GnomAD database, including 10,222 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 3652 hom., cov: 31)

Exomes 𝑓: 0.087 ( 6570 hom. )

Consequence

SLC52A1
ENST00000254853.10 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.191

Variant links:

Genes affected

SLC52A1 (HGNC:30225): (solute carrier family 52 member 1) Biological redox reactions require electron donors and acceptor. Vitamin B2 is the source for the flavin in flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) which are common redox reagents. This gene encodes a member of the riboflavin (vitamin B2) transporter family. Haploinsufficiency of this protein can cause maternal riboflavin deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2013]

SLC52A1 links:

LOC105371501 (HGNC:):

LOC105371501 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 17-5032883-A-G is Benign according to our data. Variant chr17-5032883-A-G is described in ClinVar as [Benign]. Clinvar id is 1285858.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC52A1	NM_017986.4 linkuse as main transcript	c.*74T>C		3_prime_UTR_variant	5/5	ENST00000254853.10	NP_060456.3
LOC105371501	XR_002958101.2 linkuse as main transcript	n.339+1214A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC52A1	ENST00000254853.10 linkuse as main transcript	c.*74T>C		3_prime_UTR_variant	5/5	1	NM_017986.4	ENSP00000254853	P1	Q9NWF4-1

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25154

AN:

151834

Hom.:

3648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.0725

Gnomad AMR

AF:

0.0940

Gnomad ASJ

AF:

0.0565

Gnomad EAS

AF:

0.0425

Gnomad SAS

AF:

0.0232

Gnomad FIN

AF:

0.0774

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0835

Gnomad OTH

AF:

0.133

GnomAD4 exome

AF:

0.0869

AC:

107748

AN:

1239646

Hom.:

6570

Cov.:

AF XY:

0.0840

AC XY:

51938

AN XY:

618192

show subpopulations

Gnomad4 AFR exome

AF:

0.409

Gnomad4 AMR exome

AF:

0.0549

Gnomad4 ASJ exome

AF:

0.0574

Gnomad4 EAS exome

AF:

0.0377

Gnomad4 SAS exome

AF:

0.0233

Gnomad4 FIN exome

AF:

0.0779

Gnomad4 NFE exome

AF:

0.0860

Gnomad4 OTH exome

AF:

0.0966

GnomAD4 genome

AF:

0.166

AC:

25183

AN:

151952

Hom.:

3652

Cov.:

AF XY:

0.160

AC XY:

11912

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.395

Gnomad4 AMR

AF:

0.0939

Gnomad4 ASJ

AF:

0.0565

Gnomad4 EAS

AF:

0.0424

Gnomad4 SAS

AF:

0.0232

Gnomad4 FIN

AF:

0.0774

Gnomad4 NFE

AF:

0.0834

Gnomad4 OTH

AF:

0.132

Alfa

AF:

0.121

Hom.:

405

Bravo

AF:

0.178

Asia WGS

AF:

0.0570

AC:

201

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 31, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.31

DANN

Benign

0.49

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over