rs4305983

Variant names:

• chr9-84329536-A-G
• rs4305983
• NM_001199633.2:c.60+11038T>C

Variant summary

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

The NM_001199633.2(SLC28A3):​c.60+11038T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,072 control chromosomes in the GnomAD database, including 44,310 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 0.76 (44310 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 8 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]

ENSG00000285987 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.60+11038T>C		intron_variant	Intron 1 of 17	ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.60+11038T>C		intron_variant	Intron 1 of 17	1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.86+11038T>C		intron_variant	Intron 1 of 4	3
ENSG00000285987	ENST00000650453.1	n.536+12487A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115462 AN: 151954 Hom.: 44255 Cov.: 32

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.760 AC: 115578 AN: 152072 Hom.: 44310 Cov.: 32 AF XY: 0.761 AC XY: 56527 AN XY: 74322

African (AFR) AF: 0.855 AC: 35485 AN: 41492

American (AMR) AF: 0.812 AC: 12385 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2528 AN: 3472

East Asian (EAS) AF: 0.829 AC: 4290 AN: 5178

South Asian (SAS) AF: 0.782 AC: 3769 AN: 4822

European-Finnish (FIN) AF: 0.711 AC: 7515 AN: 10564

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47164 AN: 67974

Other (OTH) AF: 0.763 AC: 1608 AN: 2108

Alfa AF: 0.713 Hom.: 84278

Bravo AF: 0.773

Asia WGS AF: 0.829 AC: 2882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.79
PhyloP100		-0.59
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: rs4305983; hg19: chr9-86944451; COSMIC: COSV66152529;