rs11140544

Positions:

• chr9-84351844-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC28A3	NM_022127.3	c.-45-11166A>C		intron_variant			NP_071410.1
SLC28A3	XM_011518906.3	c.-45-11166A>C		intron_variant			XP_011517208.1
SLC28A3	XM_011518907.3	c.-98+16608A>C		intron_variant			XP_011517209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285987	ENST00000650453.1	n.536+34795T>G		intron_variant

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

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.262

Alfa AF: 0.206 Hom.: 3930

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11140544; hg19: chr9-86966759;