chr9-84310959-G-T

Variant names:

• chr9-84310959-G-T
• rs9792596
• NM_001199633.2:c.157-1245C>A

Variant summary

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

The NM_001199633.2(SLC28A3):​c.157-1245C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,008 control chromosomes in the GnomAD database, including 4,345 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 0.23 (4345 hom., cov: 33)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 2 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.157-1245C>A		intron_variant	Intron 2 of 17	ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.157-1245C>A		intron_variant	Intron 2 of 17	1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.183-372C>A		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34693 AN: 151890 Hom.: 4325 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.229 AC: 34762 AN: 152008 Hom.: 4345 Cov.: 33 AF XY: 0.230 AC XY: 17058 AN XY: 74292

African (AFR) AF: 0.237 AC: 9801 AN: 41432

American (AMR) AF: 0.274 AC: 4189 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3472

East Asian (EAS) AF: 0.527 AC: 2724 AN: 5166

South Asian (SAS) AF: 0.259 AC: 1245 AN: 4810

European-Finnish (FIN) AF: 0.187 AC: 1967 AN: 10544

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13486 AN: 67992

Other (OTH) AF: 0.221 AC: 467 AN: 2116

Alfa AF: 0.204 Hom.: 4131

Bravo AF: 0.238

Asia WGS AF: 0.347 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.35
PhyloP100		0.017
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: rs9792596; hg19: chr9-86925874;