rs4877847

Positions:

• chr9-84331502-A-C
• chr9-84331502-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199633.2(SLC28A3):​c.60+9072T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,868 control chromosomes in the GnomAD database, including 21,265 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 0.53 (21265 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A3	NM_001199633.2	c.60+9072T>G		intron_variant		ENST00000376238.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A3	ENST00000376238.5	c.60+9072T>G		intron_variant		1	NM_001199633.2	P1
	ENST00000650453.1	n.536+14453A>C		intron_variant, non_coding_transcript_variant
SLC28A3	ENST00000495823.1	n.86+9072T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80006 AN: 151750 Hom.: 21268 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.527 AC: 80037 AN: 151868 Hom.: 21265 Cov.: 32 AF XY: 0.525 AC XY: 38924 AN XY: 74180

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.561

Alfa AF: 0.538 Hom.: 22252

Bravo AF: 0.537

Asia WGS AF: 0.427 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs4877847; hg19: chr9-86946417; COSMIC: COSV66152547;