chr9-84335955-C-T

Variant names:

• chr9-84335955-C-T
• rs4877848
• NM_001199633.2:c.60+4619G>A

Variant summary

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

The NM_022127.3(SLC28A3):​c.60+4619G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,788 control chromosomes in the GnomAD database, including 4,610 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 0.24 (4610 hom., cov: 30)
• Consequence: SLC28A3 NM_022127.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813
• 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]

ENSG00000285987 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 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.60+4619G>A		intron	N/A	NP_001186562.1
	SLC28A3	NM_022127.3		c.60+4619G>A		intron	N/A	NP_071410.1
	SLC28A3	NR_037638.3		n.185+4619G>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.60+4619G>A		intron	N/A	ENSP00000365413.4
	SLC28A3	ENST00000495823.1	TSL:3	n.86+4619G>A		intron	N/A
	ENSG00000285987	ENST00000650453.1		n.536+18906C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36225 AN: 151670 Hom.: 4609 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.239 AC: 36252 AN: 151788 Hom.: 4610 Cov.: 30 AF XY: 0.238 AC XY: 17615 AN XY: 74168

African (AFR) AF: 0.313 AC: 12953 AN: 41354

American (AMR) AF: 0.159 AC: 2422 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 799 AN: 3466

East Asian (EAS) AF: 0.249 AC: 1287 AN: 5164

South Asian (SAS) AF: 0.297 AC: 1427 AN: 4804

European-Finnish (FIN) AF: 0.244 AC: 2563 AN: 10522

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14245 AN: 67934

Other (OTH) AF: 0.209 AC: 440 AN: 2108

Alfa AF: 0.217 Hom.: 12409

Bravo AF: 0.232

Asia WGS AF: 0.281 AC: 979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.61
PhyloP100		0.81
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: rs4877848; hg19: chr9-86950870;