9-84354137-A-G

Variant names:

• chr9-84354137-A-G
• rs17087148
• NM_022127.3:c.-45-13459T>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.-45-13459T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,192 control chromosomes in the GnomAD database, including 1,531 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 (1531 hom., cov: 33)
• Consequence: SLC28A3 NM_022127.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_022127.3	c.-45-13459T>C		intron_variant	Intron 1 of 18		NP_071410.1
SLC28A3	XM_011518906.3	c.-45-13459T>C		intron_variant	Intron 1 of 18		XP_011517208.1
SLC28A3	XM_011518907.3	c.-98+14315T>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+37088A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16350 AN: 152074 Hom.: 1517 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0908

Gnomad FIN AF: 0.0630

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.108 AC: 16416 AN: 152192 Hom.: 1531 Cov.: 33 AF XY: 0.109 AC XY: 8134 AN XY: 74410

African (AFR) AF: 0.223 AC: 9259 AN: 41496

American (AMR) AF: 0.128 AC: 1957 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0351 AC: 122 AN: 3472

East Asian (EAS) AF: 0.268 AC: 1382 AN: 5164

South Asian (SAS) AF: 0.0919 AC: 443 AN: 4818

European-Finnish (FIN) AF: 0.0630 AC: 669 AN: 10614

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0344 AC: 2337 AN: 68028

Other (OTH) AF: 0.0978 AC: 207 AN: 2116

Alfa AF: 0.0628 Hom.: 818

Bravo AF: 0.123

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.7
DANN	Benign	0.85
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs17087148; hg19: chr9-86969052;