Variant chr9-84286011-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001199633.2(SLC28A3):c.1381C>T(p.Leu461=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,613,680 control chromosomes in the GnomAD database, including 19,647 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.19 ( 3142 hom., cov: 32)

Exomes 𝑓: 0.14 ( 16505 hom. )

Consequence

SLC28A3
NM_001199633.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.773

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 9-84286011-G-A is Benign according to our data. Variant chr9-84286011-G-A is described in ClinVar as [Benign]. Clinvar id is 375669.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.773 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 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.1381C>T	p.Leu461=	synonymous_variant	13/18	ENST00000376238.5	NP_001186562.1
SLC28A3-AS1	XR_001746802.1 linkuse as main transcript	n.231-3929G>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.1381C>T	p.Leu461=	synonymous_variant	13/18	1	NM_001199633.2	ENSP00000365413	P1	Q9HAS3-1
SLC28A3-AS1	ENST00000419815.1 linkuse as main transcript	n.182-3929G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

28410

AN:

152030

Hom.:

3136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.308

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.222

Gnomad EAS

AF:

0.149

Gnomad SAS

AF:

0.131

Gnomad FIN

AF:

0.0605

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.191

GnomAD3 exomes

AF:

0.153

AC:

38437

AN:

250790

Hom.:

3336

AF XY:

0.147

AC XY:

19910

AN XY:

135514

show subpopulations

Gnomad AFR exome

AF:

0.311

Gnomad AMR exome

AF:

0.199

Gnomad ASJ exome

AF:

0.213

Gnomad EAS exome

AF:

0.151

Gnomad SAS exome

AF:

0.127

Gnomad FIN exome

AF:

0.0663

Gnomad NFE exome

AF:

0.135

Gnomad OTH exome

AF:

0.159

GnomAD4 exome

AF:

0.145

AC:

211832

AN:

1461532

Hom.:

16505

Cov.:

AF XY:

0.144

AC XY:

104536

AN XY:

727050

show subpopulations

Gnomad4 AFR exome

AF:

0.322

Gnomad4 AMR exome

AF:

0.201

Gnomad4 ASJ exome

AF:

0.216

Gnomad4 EAS exome

AF:

0.116

Gnomad4 SAS exome

AF:

0.128

Gnomad4 FIN exome

AF:

0.0702

Gnomad4 NFE exome

AF:

0.140

Gnomad4 OTH exome

AF:

0.166

GnomAD4 genome

AF:

0.187

AC:

28460

AN:

152148

Hom.:

3142

Cov.:

AF XY:

0.180

AC XY:

13410

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.308

Gnomad4 AMR

AF:

0.188

Gnomad4 ASJ

AF:

0.222

Gnomad4 EAS

AF:

0.149

Gnomad4 SAS

AF:

0.132

Gnomad4 FIN

AF:

0.0605

Gnomad4 NFE

AF:

0.140

Gnomad4 OTH

AF:

0.190

Alfa

AF:

0.158

Hom.:

3835

Bravo

AF:

0.203

Asia WGS

AF:

0.163

AC:

568

AN:

3478

EpiCase

AF:

0.144

EpiControl

AF:

0.143

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 15, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

4.2

DANN

Benign

0.63

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over