rs11140523

chr9-84320669-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLC28A3	NM_001199633.2	c.61-7215C>T		intron_variant		ENST00000376238.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC28A3	ENST00000376238.5	c.61-7215C>T		intron_variant		1	NM_001199633.2	P1
	ENST00000650453.1	n.536+3620G>A		intron_variant, non_coding_transcript_variant
SLC28A3	ENST00000495823.1	n.87-7215C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0844

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0800

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.101

Alfa AF: 0.118 Hom.: 657

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs11140523; hg19: chr9-86935584;