rs4585823

Variant names:

• chr9-84289270-G-A
• rs4585823
• NM_001199633.2:c.1149+884C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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]

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199633.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	NM_001199633.2	MANE Select	c.1149+884C>T		intron	N/A	NP_001186562.1	Q9HAS3-1
	SLC28A3	NM_022127.3		c.1149+884C>T		intron	N/A	NP_071410.1	Q9HAS3-1
	SLC28A3	NR_037638.3		n.1450+884C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	ENST00000376238.5	TSL:1 MANE Select	c.1149+884C>T		intron	N/A	ENSP00000365413.4	Q9HAS3-1
	SLC28A3-AS1	ENST00000419815.1	TSL:3	n.182-670G>A		intron	N/A

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

African (AFR) AF: 0.157 AC: 6530 AN: 41466

American (AMR) AF: 0.207 AC: 3161 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3472

East Asian (EAS) AF: 0.0384 AC: 199 AN: 5176

South Asian (SAS) AF: 0.219 AC: 1055 AN: 4820

European-Finnish (FIN) AF: 0.204 AC: 2154 AN: 10560

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.132 AC: 8943 AN: 68000

Other (OTH) AF: 0.150 AC: 317 AN: 2108

Alfa AF: 0.139 Hom.: 5090

Bravo AF: 0.149

Asia WGS AF: 0.129 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.75
PhyloP100		-0.74
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: rs4585823; hg19: chr9-86904185;