rs12004882

Positions:

• chr9-84323144-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199633.2(SLC28A3):​c.61-9690G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,170 control chromosomes in the GnomAD database, including 2,502 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 0.16 (2502 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A3	NM_001199633.2	c.61-9690G>C		intron_variant		ENST00000376238.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A3	ENST00000376238.5	c.61-9690G>C		intron_variant		1	NM_001199633.2	P1
	ENST00000650453.1	n.536+6095C>G		intron_variant, non_coding_transcript_variant
SLC28A3	ENST00000495823.1	n.87-9690G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24195 AN: 152052 Hom.: 2487 Cov.: 32

Gnomad AFR AF: 0.0446

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.159 AC: 24216 AN: 152170 Hom.: 2502 Cov.: 32 AF XY: 0.163 AC XY: 12151 AN XY: 74396

Gnomad4 AFR AF: 0.0445

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.179

Alfa AF: 0.170 Hom.: 314

Bravo AF: 0.146

Asia WGS AF: 0.324 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.42
DANN	Benign	0.35

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: rs12004882; hg19: chr9-86938059;