rs13283683

chr9-84326528-G-C

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLC28A3	NM_001199633.2	c.61-13074C>G		intron_variant		ENST00000376238.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A3	ENST00000376238.5	c.61-13074C>G		intron_variant		1	NM_001199633.2	P1
	ENST00000650453.1	n.536+9479G>C		intron_variant, non_coding_transcript_variant
SLC28A3	ENST00000495823.1	n.87-13074C>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.129

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

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: rs13283683; hg19: chr9-86941443;