9-84284969-C-G

Position:

• chr9-84284969-C-G

Variant summary

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

The NM_001199633.2(SLC28A3):​c.1647+376G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,054 control chromosomes in the GnomAD database, including 12,605 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 0.36 (12605 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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]

SLC28A3-AS1 (HGNC:55460): (SLC28A3 regulatory antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC28A3	NM_001199633.2	c.1647+376G>C		intron_variant		ENST00000376238.5
SLC28A3-AS1	XR_001746802.1	n.231-4971C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A3	ENST00000376238.5	c.1647+376G>C		intron_variant		1	NM_001199633.2	P1
SLC28A3-AS1	ENST00000419815.1	n.182-4971C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54163 AN: 151936 Hom.: 12542 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.357 AC: 54298 AN: 152054 Hom.: 12605 Cov.: 32 AF XY: 0.354 AC XY: 26314 AN XY: 74316

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.331

Alfa AF: 0.150 Hom.: 304

Bravo AF: 0.383

Asia WGS AF: 0.435 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
DANN	Benign	0.54

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: rs4877831; hg19: chr9-86899884;