chr9-84302092-C-A

Position:

• chr9-84302092-C-A

Variant summary

Our verdict is Benign. Variant got -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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLC28A3	NM_001199633.2	c.524+108G>T		intron_variant		ENST00000376238.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A3	ENST00000376238.5	c.524+108G>T		intron_variant		1	NM_001199633.2	P1

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

Gnomad4 AMR exome AF: 0.0580

Gnomad4 ASJ exome AF: 0.117

Gnomad4 EAS exome AF: 0.131

Gnomad4 SAS exome AF: 0.0557

Gnomad4 FIN exome AF: 0.0172

Gnomad4 NFE exome AF: 0.0575

Gnomad4 OTH exome AF: 0.0718

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

Gnomad4 AMR AF: 0.0625

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.0626

Gnomad4 FIN AF: 0.0119

Gnomad4 NFE AF: 0.0563

Gnomad4 OTH AF: 0.0806

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

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;