chr9-84313015-C-T

Position:

• chr9-84313015-C-T

Variant summary

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

The NM_001199633.2(SLC28A3):​c.156+344G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,970 control chromosomes in the GnomAD database, including 11,397 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 0.37 (11397 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.156+344G>A		intron_variant		ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.156+344G>A		intron_variant		1	NM_001199633.2	ENSP00000365413	P1
SLC28A3	ENST00000495823.1	n.182+344G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56435 AN: 151852 Hom.: 11367 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.372 AC: 56520 AN: 151970 Hom.: 11397 Cov.: 32 AF XY: 0.372 AC XY: 27612 AN XY: 74282

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.347

Alfa AF: 0.343 Hom.: 2066

Bravo AF: 0.396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.61

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: rs10746739; hg19: chr9-86927930;