chr9-84314094-G-A

Variant names:

• chr9-84314094-G-A
• rs4877839
• NM_001199633.2:c.61-640C>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.61-640C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,106 control chromosomes in the GnomAD database, including 1,096 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 0.11 (1096 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• 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]

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 (AMR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.61-640C>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.61-640C>T		intron_variant	Intron 1 of 17	1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.87-640C>T		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17012 AN: 151988 Hom.: 1095 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.0765

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.112 AC: 17021 AN: 152106 Hom.: 1096 Cov.: 32 AF XY: 0.113 AC XY: 8370 AN XY: 74342

African (AFR) AF: 0.130 AC: 5408 AN: 41506

American (AMR) AF: 0.190 AC: 2900 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3468

East Asian (EAS) AF: 0.0900 AC: 465 AN: 5168

South Asian (SAS) AF: 0.0943 AC: 454 AN: 4814

European-Finnish (FIN) AF: 0.0765 AC: 808 AN: 10564

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0948 AC: 6445 AN: 67984

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.0879 Hom.: 344

Bravo AF: 0.122

Asia WGS AF: 0.114 AC: 396 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	4.2
DANN	Benign	0.61
PhyloP100		0.024
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: rs4877839; hg19: chr9-86929009;