rs13283683

Variant names:

• chr9-84326528-G-C
• rs13283683
• NM_001199633.2:c.61-13074C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199633.2(SLC28A3):​c.61-13074C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,006 control chromosomes in the GnomAD database, including 1,742 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 0.15 (1742 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 1 publications found

Genes affected

SLC28A3 (HGNC:16484): (solute carrier family 28 member 3) Nucleoside transporters, such as SLC28A3, regulate multiple cellular processes, including neurotransmission, vascular tone, adenosine concentration in the vicinity of cell surface receptors, and transport and metabolism of nucleoside drugs. SLC28A3 shows broad specificity for pyrimidine and purine nucleosides (Ritzel et al., 2001 [PubMed 11032837]).[supplied by OMIM, Mar 2008]

ENSG00000285987 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.61-13074C>G		intron_variant	Intron 1 of 17	ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.61-13074C>G		intron_variant	Intron 1 of 17	1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.87-13074C>G		intron_variant	Intron 1 of 4	3
ENSG00000285987	ENST00000650453.1	n.536+9479G>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22264 AN: 151888 Hom.: 1740 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.147 AC: 22276 AN: 152006 Hom.: 1742 Cov.: 32 AF XY: 0.148 AC XY: 10975 AN XY: 74308

African (AFR) AF: 0.152 AC: 6317 AN: 41458

American (AMR) AF: 0.113 AC: 1719 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 508 AN: 3462

East Asian (EAS) AF: 0.168 AC: 870 AN: 5174

South Asian (SAS) AF: 0.226 AC: 1087 AN: 4808

European-Finnish (FIN) AF: 0.184 AC: 1942 AN: 10566

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9495 AN: 67988

Other (OTH) AF: 0.129 AC: 271 AN: 2100

Alfa AF: 0.153 Hom.: 270

Bravo AF: 0.140

Asia WGS AF: 0.195 AC: 679 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		0.036
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13283683; hg19: chr9-86941443;