rs17087056

Variant names:

• chr9-84302092-C-A
• rs17087056
• NM_001199633.2:c.524+108G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-84302092-C-A
• chr9-84302092-C-T

Variant summary

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

The NM_001199633.2(SLC28A3):​c.524+108G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0583 in 1,046,196 control chromosomes in the GnomAD database, including 2,228 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 0.049 (299 hom., cov: 32)
  • Exomes 𝑓: 0.060 (1929 hom.)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.524+108G>T		intron_variant	Intron 5 of 17	ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.524+108G>T		intron_variant	Intron 5 of 17	1	NM_001199633.2	ENSP00000365413.4

Frequencies

GnomAD3 genomes AF: 0.0492 AC: 7479 AN: 152106 Hom.: 300 Cov.: 32

Gnomad AFR AF: 0.0180

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0623

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.0623

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.0814

GnomAD4 exome AF: 0.0598 AC: 53476 AN: 893972 Hom.: 1929 AF XY: 0.0601 AC XY: 27310 AN XY: 454066

Gnomad4 AFR exome AF: 0.0189 AC: 404 AN: 21346

Gnomad4 AMR exome AF: 0.0580 AC: 1537 AN: 26490

Gnomad4 ASJ exome AF: 0.117 AC: 2006 AN: 17198

Gnomad4 EAS exome AF: 0.131 AC: 4756 AN: 36252

Gnomad4 SAS exome AF: 0.0557 AC: 3258 AN: 58522

Gnomad4 FIN exome AF: 0.0172 AC: 626 AN: 36442

Gnomad4 NFE exome AF: 0.0575 AC: 37498 AN: 652374

Gnomad4 Remaining exome AF: 0.0718 AC: 2937 AN: 40928

GnomAD4 genome AF: 0.0491 AC: 7481 AN: 152224 Hom.: 299 Cov.: 32 AF XY: 0.0483 AC XY: 3595 AN XY: 74412

Gnomad4 AFR AF: 0.0180 AC: 0.0180085 AN: 0.0180085

Gnomad4 AMR AF: 0.0625 AC: 0.0625 AN: 0.0625

Gnomad4 ASJ AF: 0.117 AC: 0.116715 AN: 0.116715

Gnomad4 EAS AF: 0.171 AC: 0.17092 AN: 0.17092

Gnomad4 SAS AF: 0.0626 AC: 0.0625777 AN: 0.0625777

Gnomad4 FIN AF: 0.0119 AC: 0.0118846 AN: 0.0118846

Gnomad4 NFE AF: 0.0563 AC: 0.0563333 AN: 0.0563333

Gnomad4 OTH AF: 0.0806 AC: 0.0805687 AN: 0.0805687

Alfa AF: 0.0505 Hom.: 27

Bravo AF: 0.0524

Asia WGS AF: 0.111 AC: 387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.7
DANN	Benign	0.78
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

Publications

LitVar

Other links and lift over

dbSNP: rs17087056; hg19: chr9-86917007; COSMIC: COSV66154468; COSMIC: COSV66154468;