9-84318490-G-A

Position:

• chr9-84318490-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• 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/exons	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.61-5036C>T		intron_variant		ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.61-5036C>T		intron_variant		1	NM_001199633.2	ENSP00000365413	P1
	ENST00000650453.1	n.536+1441G>A		intron_variant, non_coding_transcript_variant
SLC28A3	ENST00000495823.1	n.87-5036C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.0793

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0818

Gnomad4 OTH AF: 0.175

Alfa AF: 0.0997 Hom.: 2423

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

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: rs7035188; hg19: chr9-86933405;