rs17343066

Variant names:

• chr9-84331158-G-A
• rs17343066
• NM_001199633.2:c.60+9416C>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.60+9416C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 152,030 control chromosomes in the GnomAD database, including 14,875 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 0.41 (14875 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659
• Publications: 5 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]

ENSG00000285987 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.60+9416C>T		intron_variant	Intron 1 of 17	ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.60+9416C>T		intron_variant	Intron 1 of 17	1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.86+9416C>T		intron_variant	Intron 1 of 4	3
ENSG00000285987	ENST00000650453.1	n.536+14109G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62299 AN: 151912 Hom.: 14882 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.410 AC: 62296 AN: 152030 Hom.: 14875 Cov.: 32 AF XY: 0.411 AC XY: 30568 AN XY: 74292

African (AFR) AF: 0.158 AC: 6549 AN: 41468

American (AMR) AF: 0.512 AC: 7832 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1915 AN: 3472

East Asian (EAS) AF: 0.335 AC: 1728 AN: 5156

South Asian (SAS) AF: 0.435 AC: 2098 AN: 4818

European-Finnish (FIN) AF: 0.471 AC: 4973 AN: 10558

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.522 AC: 35484 AN: 67958

Other (OTH) AF: 0.475 AC: 1001 AN: 2108

Alfa AF: 0.496 Hom.: 32810

Bravo AF: 0.401

Asia WGS AF: 0.363 AC: 1264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.59
PhyloP100		0.66
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: rs17343066; hg19: chr9-86946073;