rs11140525

Variant names:

• chr9-84322400-G-A
• rs11140525
• NM_001199633.2:c.61-8946C>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.61-8946C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,156 control chromosomes in the GnomAD database, including 15,342 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 0.40 (15342 hom., cov: 33)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	NM_001199633.2	MANE Select	c.61-8946C>T		intron	N/A	NP_001186562.1	Q9HAS3-1
	SLC28A3	NM_022127.3		c.61-8946C>T		intron	N/A	NP_071410.1	Q9HAS3-1
	SLC28A3	NR_037638.3		n.186-8946C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	ENST00000376238.5	TSL:1 MANE Select	c.61-8946C>T		intron	N/A	ENSP00000365413.4	Q9HAS3-1
	SLC28A3	ENST00000495823.1	TSL:3	n.87-8946C>T		intron	N/A
	ENSG00000285987	ENST00000650453.1		n.536+5351G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60935 AN: 152038 Hom.: 15319 Cov.: 33

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.401 AC: 61006 AN: 152156 Hom.: 15342 Cov.: 33 AF XY: 0.394 AC XY: 29346 AN XY: 74392

African (AFR) AF: 0.714 AC: 29630 AN: 41498

American (AMR) AF: 0.419 AC: 6407 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1230 AN: 3472

East Asian (EAS) AF: 0.260 AC: 1345 AN: 5180

South Asian (SAS) AF: 0.256 AC: 1232 AN: 4810

European-Finnish (FIN) AF: 0.202 AC: 2143 AN: 10598

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18112 AN: 67992

Other (OTH) AF: 0.357 AC: 755 AN: 2114

Alfa AF: 0.316 Hom.: 16494

Bravo AF: 0.434

Asia WGS AF: 0.279 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.5
DANN	Benign	0.74
PhyloP100		0.63
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: rs11140525; hg19: chr9-86937315;