rs885004

Positions:

• chr9-84294635-G-A
• chr9-84294635-G-C

Variant summary

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

The NM_001199633.2(SLC28A3):​c.862-360C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,208 control chromosomes in the GnomAD database, including 1,138 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 0.12 (1138 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.967

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.862-360C>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.862-360C>T		intron_variant		1	NM_001199633.2	ENSP00000365413	P1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18116 AN: 152090 Hom.: 1134 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.119 AC: 18142 AN: 152208 Hom.: 1138 Cov.: 32 AF XY: 0.115 AC XY: 8591 AN XY: 74408

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0539

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.143

Alfa AF: 0.132 Hom.: 1971

Bravo AF: 0.126

Asia WGS AF: 0.149 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.29

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: rs885004; hg19: chr9-86909550;