9-84284969-C-G

Variant names:

• chr9-84284969-C-G
• rs4877831
• NM_001199633.2:c.1647+376G>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.1647+376G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,054 control chromosomes in the GnomAD database, including 12,605 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 0.36 (12605 hom., cov: 32)
• Consequence: SLC28A3 NM_022127.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 8 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]

SLC28A3-AS1 (HGNC:55460): (SLC28A3 regulatory antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022127.3. 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.1647+376G>C		intron	N/A	NP_001186562.1
	SLC28A3	NM_022127.3		c.1647+376G>C		intron	N/A	NP_071410.1
	SLC28A3	NR_037638.3		n.1948+376G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	ENST00000376238.5	TSL:1 MANE Select	c.1647+376G>C		intron	N/A	ENSP00000365413.4
	SLC28A3-AS1	ENST00000419815.1	TSL:3	n.182-4971C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54163 AN: 151936 Hom.: 12542 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.357 AC: 54298 AN: 152054 Hom.: 12605 Cov.: 32 AF XY: 0.354 AC XY: 26314 AN XY: 74316

African (AFR) AF: 0.644 AC: 26717 AN: 41482

American (AMR) AF: 0.332 AC: 5076 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3470

East Asian (EAS) AF: 0.563 AC: 2910 AN: 5166

South Asian (SAS) AF: 0.293 AC: 1410 AN: 4814

European-Finnish (FIN) AF: 0.201 AC: 2121 AN: 10568

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14253 AN: 67970

Other (OTH) AF: 0.331 AC: 698 AN: 2110

Alfa AF: 0.150 Hom.: 304

Bravo AF: 0.383

Asia WGS AF: 0.435 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
DANN	Benign	0.54
PhyloP100		-0.011
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: rs4877831; hg19: chr9-86899884;