rs4877832

Positions:

• chr9-84285032-A-C

Variant summary

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

The ENST00000376238.5(SLC28A3):​c.1647+313T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,992 control chromosomes in the GnomAD database, including 23,423 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 0.52 (23423 hom., cov: 32)
• Consequence: SLC28A3 ENST00000376238.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522

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]

SLC28A3-AS1 (HGNC:55460): (SLC28A3 regulatory antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.1647+313T>G		intron_variant		ENST00000376238.5	NP_001186562.1
SLC28A3-AS1	XR_001746802.1	n.231-4908A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.1647+313T>G		intron_variant		1	NM_001199633.2	ENSP00000365413	P1
SLC28A3-AS1	ENST00000419815.1	n.182-4908A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78630 AN: 151874 Hom.: 23356 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.518 AC: 78761 AN: 151992 Hom.: 23423 Cov.: 32 AF XY: 0.520 AC XY: 38614 AN XY: 74282

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.489

Alfa AF: 0.457 Hom.: 2198

Bravo AF: 0.541

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.50

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: rs4877832; hg19: chr9-86899947;