rs17087049

Positions:

• chr9-84299457-A-G
• chr9-84299457-A-T

Variant summary

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

The NM_001199633.2(SLC28A3):​c.669+124T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0408 in 1,273,650 control chromosomes in the GnomAD database, including 5,172 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 0.11 (2041 hom., cov: 32)
  • Exomes 𝑓: 0.032 (3131 hom.)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.669+124T>C		intron_variant		ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.669+124T>C		intron_variant		1	NM_001199633.2	ENSP00000365413.4

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16317 AN: 152098 Hom.: 2026 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00870

Gnomad OTH AF: 0.0765

GnomAD4 exome AF: 0.0318 AC: 35640 AN: 1121434 Hom.: 3131 AF XY: 0.0320 AC XY: 17957 AN XY: 560954

Gnomad4 AFR exome AF: 0.301

Gnomad4 AMR exome AF: 0.161

Gnomad4 ASJ exome AF: 0.00939

Gnomad4 EAS exome AF: 0.266

Gnomad4 SAS exome AF: 0.0825

Gnomad4 FIN exome AF: 0.0167

Gnomad4 NFE exome AF: 0.00770

Gnomad4 OTH exome AF: 0.0457

GnomAD4 genome AF: 0.108 AC: 16371 AN: 152216 Hom.: 2041 Cov.: 32 AF XY: 0.109 AC XY: 8095 AN XY: 74430

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.0867

Gnomad4 FIN AF: 0.0164

Gnomad4 NFE AF: 0.00869

Gnomad4 OTH AF: 0.0752

Alfa AF: 0.0271 Hom.: 637

Bravo AF: 0.127

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.64

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: rs17087049; hg19: chr9-86914372;