rs12000457

Variant names:

• chr9-84329510-G-A
• rs12000457
• NM_001199633.2:c.60+11064C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-84329510-G-A
• chr9-84329510-G-C
• chr9-84329510-G-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.60+11064C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,148 control chromosomes in the GnomAD database, including 2,748 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 0.11 (2748 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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.60+11064C>T		intron	N/A	NP_001186562.1
	SLC28A3	NM_022127.3		c.60+11064C>T		intron	N/A	NP_071410.1
	SLC28A3	NR_037638.3		n.185+11064C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	ENST00000376238.5	TSL:1 MANE Select	c.60+11064C>T		intron	N/A	ENSP00000365413.4
	SLC28A3	ENST00000495823.1	TSL:3	n.86+11064C>T		intron	N/A
	ENSG00000285987	ENST00000650453.1		n.536+12461G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16294 AN: 152030 Hom.: 2743 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0466

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.0195

Gnomad FIN AF: 0.000756

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00435

Gnomad OTH AF: 0.0735

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

GnomAD4 genome AF: 0.107 AC: 16321 AN: 152148 Hom.: 2748 Cov.: 32 AF XY: 0.103 AC XY: 7636 AN XY: 74386

African (AFR) AF: 0.358 AC: 14826 AN: 41456

American (AMR) AF: 0.0465 AC: 710 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3472

East Asian (EAS) AF: 0.0363 AC: 188 AN: 5182

South Asian (SAS) AF: 0.0188 AC: 91 AN: 4828

European-Finnish (FIN) AF: 0.000756 AC: 8 AN: 10576

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00435 AC: 296 AN: 68028

Other (OTH) AF: 0.0728 AC: 154 AN: 2116

Alfa AF: 0.0985 Hom.: 1770

Bravo AF: 0.123

Asia WGS AF: 0.0490 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		-0.11
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: rs12000457; hg19: chr9-86944425;