rs11140523

Variant names:

• chr9-84320669-G-A
• rs11140523
• NM_001199633.2:c.61-7215C>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.61-7215C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,130 control chromosomes in the GnomAD database, including 893 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 (893 hom., cov: 30)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.61-7215C>T		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.61-7215C>T		intron_variant	Intron 1 of 17	1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.87-7215C>T		intron_variant	Intron 1 of 4	3
ENSG00000285987	ENST00000650453.1	n.536+3620G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16050 AN: 152012 Hom.: 890 Cov.: 30

Gnomad AFR AF: 0.0839

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0800

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.106 AC: 16083 AN: 152130 Hom.: 893 Cov.: 30 AF XY: 0.102 AC XY: 7617 AN XY: 74378

African (AFR) AF: 0.0844 AC: 3502 AN: 41482

American (AMR) AF: 0.131 AC: 1998 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3470

East Asian (EAS) AF: 0.124 AC: 640 AN: 5162

South Asian (SAS) AF: 0.106 AC: 510 AN: 4822

European-Finnish (FIN) AF: 0.0800 AC: 849 AN: 10612

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.115 AC: 7848 AN: 67996

Other (OTH) AF: 0.101 AC: 213 AN: 2110

Alfa AF: 0.116 Hom.: 787

Bravo AF: 0.109

Asia WGS AF: 0.108 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.071
DANN	Benign	0.55
PhyloP100		-0.74
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: rs11140523; hg19: chr9-86935584;