9-84307121-C-T

Variant names:

• chr9-84307121-C-T
• rs10123041
• NM_001199633.2:c.243-1776G>A

Variant summary

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

The NM_001199633.2(SLC28A3):​c.243-1776G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 142,168 control chromosomes in the GnomAD database, including 2,816 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 0.19 (2816 hom., cov: 23)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	NM_001199633.2	MANE Select	c.243-1776G>A		intron	N/A	NP_001186562.1
	SLC28A3	NM_022127.3		c.243-1776G>A		intron	N/A	NP_071410.1
	SLC28A3	NR_037638.3		n.544-1776G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	ENST00000376238.5	TSL:1 MANE Select	c.243-1776G>A		intron	N/A	ENSP00000365413.4
	SLC28A3	ENST00000495823.1	TSL:3	n.445-1776G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 26632 AN: 142106 Hom.: 2813 Cov.: 23

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.187 AC: 26642 AN: 142168 Hom.: 2816 Cov.: 23 AF XY: 0.185 AC XY: 12687 AN XY: 68692

African (AFR) AF: 0.257 AC: 9603 AN: 37354

American (AMR) AF: 0.224 AC: 3179 AN: 14190

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 488 AN: 3422

East Asian (EAS) AF: 0.107 AC: 535 AN: 4984

South Asian (SAS) AF: 0.165 AC: 743 AN: 4498

European-Finnish (FIN) AF: 0.149 AC: 1288 AN: 8662

Middle Eastern (MID) AF: 0.167 AC: 47 AN: 282

European-Non Finnish (NFE) AF: 0.157 AC: 10340 AN: 65940

Other (OTH) AF: 0.194 AC: 377 AN: 1944

Alfa AF: 0.544 Hom.: 6611

Asia WGS AF: 0.137 AC: 462 AN: 3376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		0.28
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: rs10123041; hg19: chr9-86922036;