9-84340242-C-T

Variant names:

• chr9-84340242-C-T
• rs3812509
• NM_001199633.2:c.60+332G>A

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+332G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,818 control chromosomes in the GnomAD database, including 27,145 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 0.60 (27145 hom., cov: 30)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.60+332G>A		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+332G>A		intron_variant	Intron 1 of 17	1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.86+332G>A		intron_variant	Intron 1 of 4	3
ENSG00000285987	ENST00000650453.1	n.536+23193C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90338 AN: 151700 Hom.: 27134 Cov.: 30

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.595 AC: 90392 AN: 151818 Hom.: 27145 Cov.: 30 AF XY: 0.593 AC XY: 43993 AN XY: 74192

African (AFR) AF: 0.551 AC: 22815 AN: 41416

American (AMR) AF: 0.657 AC: 10034 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2377 AN: 3466

East Asian (EAS) AF: 0.434 AC: 2224 AN: 5122

South Asian (SAS) AF: 0.569 AC: 2741 AN: 4814

European-Finnish (FIN) AF: 0.533 AC: 5615 AN: 10526

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42467 AN: 67900

Other (OTH) AF: 0.639 AC: 1345 AN: 2106

Alfa AF: 0.627 Hom.: 49916

Bravo AF: 0.599

Asia WGS AF: 0.512 AC: 1782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.5
DANN	Benign	0.61
PhyloP100		-0.80
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: rs3812509; hg19: chr9-86955157;