chr9-84285032-A-C

Variant names:

• chr9-84285032-A-C
• rs4877832
• NM_001199633.2:c.1647+313T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199633.2(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 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 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.1647+313T>G		intron	N/A	NP_001186562.1	Q9HAS3-1
	SLC28A3	NM_022127.3		c.1647+313T>G		intron	N/A	NP_071410.1	Q9HAS3-1
	SLC28A3	NR_037638.3		n.1948+313T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	ENST00000376238.5	TSL:1 MANE Select	c.1647+313T>G		intron	N/A	ENSP00000365413.4	Q9HAS3-1
	SLC28A3-AS1	ENST00000419815.1	TSL:3	n.182-4908A>C		intron	N/A

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

African (AFR) AF: 0.814 AC: 33739 AN: 41470

American (AMR) AF: 0.544 AC: 8293 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1472 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3075 AN: 5170

South Asian (SAS) AF: 0.513 AC: 2468 AN: 4808

European-Finnish (FIN) AF: 0.410 AC: 4326 AN: 10558

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24104 AN: 67956

Other (OTH) AF: 0.489 AC: 1033 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.50
PhyloP100		-0.52
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: rs4877832; hg19: chr9-86899947;