17-5032883-A-G

Variant summary

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

The NM_017986.4(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 NM_017986.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.191

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]

LOC105371501 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 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_single_submitter, 1 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	UniProt
SLC52A1	NM_017986.4	c.*74T>C		3_prime_UTR_variant	5/5	ENST00000254853.10
LOC105371501	XR_002958101.2	n.339+1214A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC52A1	ENST00000254853.10	c.*74T>C		3_prime_UTR_variant	5/5	1	NM_017986.4	P1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25154 AN: 151834 Hom.: 3648 Cov.: 31

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.: 18 AF XY: 0.0840 AC XY: 51938 AN XY: 618192

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.: 31 AF XY: 0.160 AC XY: 11912 AN XY: 74272

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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

Other links and lift over

dbSNP: rs60480329; hg19: chr17-4936178; COSMIC: COSV54692597; COSMIC: COSV54692597;