rs11140544

Variant names:

• chr9-84351844-T-G
• rs11140544
• NM_022127.3:c.-45-11166A>C

Variant summary

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

The NM_022127.3(SLC28A3):​c.-45-11166A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 150,596 control chromosomes in the GnomAD database, including 11,059 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 0.32 (11059 hom., cov: 30)
• Consequence: SLC28A3 NM_022127.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 6 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 = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_022127.3	c.-45-11166A>C		intron_variant	Intron 1 of 18		NP_071410.1
SLC28A3	XM_011518906.3	c.-45-11166A>C		intron_variant	Intron 1 of 18		XP_011517208.1
SLC28A3	XM_011518907.3	c.-98+16608A>C		intron_variant	Intron 1 of 16		XP_011517209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285987	ENST00000650453.1	n.536+34795T>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.324 AC: 48735 AN: 150488 Hom.: 11037 Cov.: 30

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.0914

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.216

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.324 AC: 48805 AN: 150596 Hom.: 11059 Cov.: 30 AF XY: 0.322 AC XY: 23674 AN XY: 73480

African (AFR) AF: 0.641 AC: 26354 AN: 41094

American (AMR) AF: 0.192 AC: 2892 AN: 15080

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3462

East Asian (EAS) AF: 0.355 AC: 1813 AN: 5106

South Asian (SAS) AF: 0.297 AC: 1416 AN: 4764

European-Finnish (FIN) AF: 0.246 AC: 2480 AN: 10084

Middle Eastern (MID) AF: 0.226 AC: 65 AN: 288

European-Non Finnish (NFE) AF: 0.185 AC: 12542 AN: 67724

Other (OTH) AF: 0.262 AC: 546 AN: 2086

Alfa AF: 0.219 Hom.: 5959

Bravo AF: 0.333

Asia WGS AF: 0.340 AC: 1176 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.77
PhyloP100		-0.079

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11140544; hg19: chr9-86966759;