9-84318490-G-A

Variant names:

• chr9-84318490-G-A
• rs7035188
• NM_001199633.2:c.61-5036C>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.61-5036C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,036 control chromosomes in the GnomAD database, including 5,809 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 0.21 (5809 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.61-5036C>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.61-5036C>T		intron_variant	Intron 1 of 17	1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.87-5036C>T		intron_variant	Intron 1 of 4	3
ENSG00000285987	ENST00000650453.1	n.536+1441G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32511 AN: 151918 Hom.: 5772 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0819

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.214 AC: 32606 AN: 152036 Hom.: 5809 Cov.: 32 AF XY: 0.214 AC XY: 15944 AN XY: 74354

African (AFR) AF: 0.478 AC: 19781 AN: 41424

American (AMR) AF: 0.175 AC: 2677 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 275 AN: 3470

East Asian (EAS) AF: 0.364 AC: 1889 AN: 5186

South Asian (SAS) AF: 0.178 AC: 855 AN: 4814

European-Finnish (FIN) AF: 0.106 AC: 1122 AN: 10574

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0818 AC: 5565 AN: 67992

Other (OTH) AF: 0.175 AC: 369 AN: 2112

Alfa AF: 0.120 Hom.: 8489

Bravo AF: 0.233

Asia WGS AF: 0.263 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.56
PhyloP100		0.40
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: rs7035188; hg19: chr9-86933405;