rs4585823

Positions:

• chr9-84289270-G-A

Variant summary

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

The NM_001199633.2(SLC28A3):​c.1149+884C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,086 control chromosomes in the GnomAD database, including 1,923 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 (1923 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A3	NM_001199633.2	c.1149+884C>T		intron_variant		ENST00000376238.5
SLC28A3-AS1	XR_001746802.1	n.231-670G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A3	ENST00000376238.5	c.1149+884C>T		intron_variant		1	NM_001199633.2	P1
SLC28A3-AS1	ENST00000419815.1	n.182-670G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22960 AN: 151968 Hom.: 1924 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.151 AC: 22950 AN: 152086 Hom.: 1923 Cov.: 32 AF XY: 0.157 AC XY: 11653 AN XY: 74324

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.0384

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.150

Alfa AF: 0.139 Hom.: 2292

Bravo AF: 0.149

Asia WGS AF: 0.129 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.75

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: rs4585823; hg19: chr9-86904185;