rs4877847

Variant names:

• chr9-84331502-A-C
• rs4877847
• NM_001199633.2:c.60+9072T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-84331502-A-C
• chr9-84331502-A-G

Variant summary

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

The NM_001199633.2(SLC28A3):​c.60+9072T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,868 control chromosomes in the GnomAD database, including 21,265 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 0.53 (21265 hom., cov: 32)
• Consequence: SLC28A3 NM_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 14 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.58 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.60+9072T>G		intron	N/A	NP_001186562.1
	SLC28A3	NM_022127.3		c.60+9072T>G		intron	N/A	NP_071410.1
	SLC28A3	NR_037638.3		n.185+9072T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A3	ENST00000376238.5	TSL:1 MANE Select	c.60+9072T>G		intron	N/A	ENSP00000365413.4
	SLC28A3	ENST00000495823.1	TSL:3	n.86+9072T>G		intron	N/A
	ENSG00000285987	ENST00000650453.1		n.536+14453A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80006 AN: 151750 Hom.: 21268 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.527 AC: 80037 AN: 151868 Hom.: 21265 Cov.: 32 AF XY: 0.525 AC XY: 38924 AN XY: 74180

African (AFR) AF: 0.535 AC: 22139 AN: 41404

American (AMR) AF: 0.590 AC: 8993 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1952 AN: 3472

East Asian (EAS) AF: 0.404 AC: 2079 AN: 5146

South Asian (SAS) AF: 0.456 AC: 2198 AN: 4816

European-Finnish (FIN) AF: 0.472 AC: 4961 AN: 10512

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35808 AN: 67962

Other (OTH) AF: 0.561 AC: 1180 AN: 2104

Alfa AF: 0.536 Hom.: 38041

Bravo AF: 0.537

Asia WGS AF: 0.427 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.71
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: rs4877847; hg19: chr9-86946417; COSMIC: COSV66152547;