rs10122651

Variant names:

• chr9-84318969-A-C
• rs10122651
• NM_001199633.2:c.61-5515T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-84318969-A-C
• chr9-84318969-A-T

Variant summary

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

The NM_001199633.2(SLC28A3):​c.61-5515T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,998 control chromosomes in the GnomAD database, including 13,922 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 (13922 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 3 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]

ENSG00000285987 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199633.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	NM_001199633.2	MANE Select	c.61-5515T>G		intron	N/A	NP_001186562.1
	SLC28A3	NM_022127.3		c.61-5515T>G		intron	N/A	NP_071410.1
	SLC28A3	NR_037638.3		n.186-5515T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	ENST00000376238.5	TSL:1 MANE Select	c.61-5515T>G		intron	N/A	ENSP00000365413.4
	SLC28A3	ENST00000495823.1	TSL:3	n.87-5515T>G		intron	N/A
	ENSG00000285987	ENST00000650453.1		n.536+1920A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54327 AN: 151878 Hom.: 13875 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.358 AC: 54428 AN: 151998 Hom.: 13922 Cov.: 32 AF XY: 0.358 AC XY: 26600 AN XY: 74314

African (AFR) AF: 0.711 AC: 29427 AN: 41366

American (AMR) AF: 0.378 AC: 5774 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2486 AN: 5162

South Asian (SAS) AF: 0.270 AC: 1302 AN: 4826

European-Finnish (FIN) AF: 0.183 AC: 1937 AN: 10594

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

European-Non Finnish (NFE) AF: 0.179 AC: 12201 AN: 67986

Other (OTH) AF: 0.307 AC: 648 AN: 2112

Alfa AF: 0.239 Hom.: 14302

Bravo AF: 0.392

Asia WGS AF: 0.385 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.62
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: rs10122651; hg19: chr9-86933884;