chr9-84302092-C-A

Variant names:

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

African (AFR) AF: 0.0189 AC: 404 AN: 21346

American (AMR) AF: 0.0580 AC: 1537 AN: 26490

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 2006 AN: 17198

East Asian (EAS) AF: 0.131 AC: 4756 AN: 36252

South Asian (SAS) AF: 0.0557 AC: 3258 AN: 58522

European-Finnish (FIN) AF: 0.0172 AC: 626 AN: 36442

Middle Eastern (MID) AF: 0.103 AC: 454 AN: 4420

European-Non Finnish (NFE) AF: 0.0575 AC: 37498 AN: 652374

Other (OTH) 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

African (AFR) AF: 0.0180 AC: 748 AN: 41536

American (AMR) AF: 0.0625 AC: 956 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3470

East Asian (EAS) AF: 0.171 AC: 884 AN: 5172

South Asian (SAS) AF: 0.0626 AC: 302 AN: 4826

European-Finnish (FIN) AF: 0.0119 AC: 126 AN: 10602

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0563 AC: 3831 AN: 68006

Other (OTH) AF: 0.0806 AC: 170 AN: 2110

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
PhyloP100		-0.010
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: rs17087056; hg19: chr9-86917007; COSMIC: COSV66154468; COSMIC: COSV66154468;