chr9-84335955-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199633.2(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_001199633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A3	NM_001199633.2	c.60+4619G>A		intron_variant	Intron 1 of 17	ENST00000376238.5	NP_001186562.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5	c.60+4619G>A		intron_variant	Intron 1 of 17	1	NM_001199633.2	ENSP00000365413.4
SLC28A3	ENST00000495823.1	n.86+4619G>A		intron_variant	Intron 1 of 4	3
ENSG00000285987	ENST00000650453.1	n.536+18906C>T		intron_variant	Intron 1 of 6

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

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.209

Alfa AF: 0.212 Hom.: 5142

Bravo AF: 0.232

Asia WGS AF: 0.281 AC: 979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs4877848; hg19: chr9-86950870;