Variant 9-84285454-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001199633.2(SLC28A3):c.1538A>T(p.Tyr513Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0661 in 1,614,062 control chromosomes in the GnomAD database, including 4,117 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.091 ( 756 hom., cov: 32)

Exomes 𝑓: 0.064 ( 3361 hom. )

Consequence

SLC28A3
NM_001199633.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.48

Variant links:

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 links:

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

SLC28A3-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004617244).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC28A3	NM_001199633.2 linkuse as main transcript	c.1538A>T	p.Tyr513Phe	missense_variant	14/18	ENST00000376238.5	NP_001186562.1
SLC28A3-AS1	XR_001746802.1 linkuse as main transcript	n.231-4486T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC28A3	ENST00000376238.5 linkuse as main transcript	c.1538A>T	p.Tyr513Phe	missense_variant	14/18	1	NM_001199633.2	ENSP00000365413	P1	Q9HAS3-1
SLC28A3-AS1	ENST00000419815.1 linkuse as main transcript	n.182-4486T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0906

AC:

13785

AN:

152090

Hom.:

752

Cov.:

show subpopulations

Gnomad AFR

AF:

0.152

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0484

Gnomad ASJ

AF:

0.0490

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.0784

Gnomad FIN

AF:

0.126

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0605

Gnomad OTH

AF:

0.0798

GnomAD3 exomes

AF:

0.0724

AC:

18178

AN:

251240

Hom.:

803

AF XY:

0.0723

AC XY:

9811

AN XY:

135770

show subpopulations

Gnomad AFR exome

AF:

0.154

Gnomad AMR exome

AF:

0.0282

Gnomad ASJ exome

AF:

0.0492

Gnomad EAS exome

AF:

0.114

Gnomad SAS exome

AF:

0.0764

Gnomad FIN exome

AF:

0.127

Gnomad NFE exome

AF:

0.0581

Gnomad OTH exome

AF:

0.0697

GnomAD4 exome

AF:

0.0636

AC:

92958

AN:

1461854

Hom.:

3361

Cov.:

AF XY:

0.0636

AC XY:

46236

AN XY:

727220

show subpopulations

Gnomad4 AFR exome

AF:

0.150

Gnomad4 AMR exome

AF:

0.0306

Gnomad4 ASJ exome

AF:

0.0475

Gnomad4 EAS exome

AF:

0.0910

Gnomad4 SAS exome

AF:

0.0746

Gnomad4 FIN exome

AF:

0.127

Gnomad4 NFE exome

AF:

0.0576

Gnomad4 OTH exome

AF:

0.0688

GnomAD4 genome

AF:

0.0907

AC:

13809

AN:

152208

Hom.:

756

Cov.:

AF XY:

0.0923

AC XY:

6864

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.152

Gnomad4 AMR

AF:

0.0482

Gnomad4 ASJ

AF:

0.0490

Gnomad4 EAS

AF:

0.103

Gnomad4 SAS

AF:

0.0795

Gnomad4 FIN

AF:

0.126

Gnomad4 NFE

AF:

0.0604

Gnomad4 OTH

AF:

0.0851

Alfa

AF:

0.0564

Hom.:

223

Bravo

AF:

0.0874

TwinsUK

AF:

0.0607

AC:

225

ALSPAC

AF:

0.0576

AC:

222

ESP6500AA

AF:

0.147

AC:

647

ESP6500EA

AF:

0.0571

AC:

491

ExAC

AF:

0.0746

AC:

9054

Asia WGS

AF:

0.100

AC:

352

AN:

3478

EpiCase

AF:

0.0533

EpiControl

AF:

0.0501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.46

CADD

Uncertain

DANN

Uncertain

0.98

DEOGEN2

Benign

0.010

Eigen

Uncertain

0.41

Eigen_PC

Uncertain

0.44

FATHMM_MKL

Uncertain

0.85

LIST_S2

Uncertain

0.97

MetaRNN

Benign

0.0046

MetaSVM

Benign

-0.95

MutationAssessor

Uncertain

2.9

MutationTaster

Benign

0.17

P;P

PrimateAI

Benign

0.42

PROVEAN

Benign

-1.3

REVEL

Benign

0.083

Sift

Benign

0.26

Sift4G

Benign

0.44

Polyphen

0.90

Vest4

0.16

MPC

0.68

ClinPred

0.083

GERP RS

5.7

Varity_R

0.46

gMVP

0.56

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over