rs10780663

Variant names:

• chr9-84316147-A-G
• rs10780663
• NM_001199633.2:c.61-2693T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199633.2(SLC28A3):​c.61-2693T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,060 control chromosomes in the GnomAD database, including 13,250 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 0.35 (13250 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.955
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.61-2693T>C		intron_variant	Intron 1 of 17	ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.61-2693T>C		intron_variant	Intron 1 of 17	1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.87-2693T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53391 AN: 151942 Hom.: 13211 Cov.: 32

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.352 AC: 53483 AN: 152060 Hom.: 13250 Cov.: 32 AF XY: 0.352 AC XY: 26205 AN XY: 74350

African (AFR) AF: 0.688 AC: 28521 AN: 41450

American (AMR) AF: 0.377 AC: 5770 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3472

East Asian (EAS) AF: 0.475 AC: 2449 AN: 5152

South Asian (SAS) AF: 0.271 AC: 1307 AN: 4826

European-Finnish (FIN) AF: 0.184 AC: 1947 AN: 10580

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12201 AN: 67972

Other (OTH) AF: 0.301 AC: 635 AN: 2110

Alfa AF: 0.225 Hom.: 7361

Bravo AF: 0.384

Asia WGS AF: 0.380 AC: 1320 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	0.68
DANN	Benign	0.81
PhyloP100		-0.95
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10780663; hg19: chr9-86931062;