rs4305983

chr9-84329536-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLC28A3	NM_001199633.2	c.60+11038T>C		intron_variant		ENST00000376238.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A3	ENST00000376238.5	c.60+11038T>C		intron_variant		1	NM_001199633.2	P1
	ENST00000650453.1	n.536+12487A>G		intron_variant, non_coding_transcript_variant
SLC28A3	ENST00000495823.1	n.86+11038T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.763

Alfa AF: 0.712 Hom.: 29473

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

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: rs4305983; hg19: chr9-86944451; COSMIC: COSV66152529;