rs11140525

Positions:

• chr9-84322400-G-A

Variant summary

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

The NM_001199633.2(SLC28A3):​c.61-8946C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,156 control chromosomes in the GnomAD database, including 15,342 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 0.40 (15342 hom., cov: 33)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.61-8946C>T		intron_variant		ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.61-8946C>T		intron_variant		1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.87-8946C>T		intron_variant		3
ENSG00000285987	ENST00000650453.1	n.536+5351G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60935 AN: 152038 Hom.: 15319 Cov.: 33

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.401 AC: 61006 AN: 152156 Hom.: 15342 Cov.: 33 AF XY: 0.394 AC XY: 29346 AN XY: 74392

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.357

Alfa AF: 0.297 Hom.: 10165

Bravo AF: 0.434

Asia WGS AF: 0.279 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.5
DANN	Benign	0.74

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: rs11140525; hg19: chr9-86937315;