9-84307121-C-T

Position:

• chr9-84307121-C-T

Variant summary

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

The NM_001199633.2(SLC28A3):​c.243-1776G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 142,168 control chromosomes in the GnomAD database, including 2,816 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 0.19 (2816 hom., cov: 23)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.243-1776G>A		intron_variant		ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.243-1776G>A		intron_variant		1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.445-1776G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.187 AC: 26632 AN: 142106 Hom.: 2813 Cov.: 23

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.187 AC: 26642 AN: 142168 Hom.: 2816 Cov.: 23 AF XY: 0.185 AC XY: 12687 AN XY: 68692

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.194

Alfa AF: 0.0479 Hom.: 53

Asia WGS AF: 0.137 AC: 462 AN: 3376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.72

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: rs10123041; hg19: chr9-86922036;