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rs7853758

chr9-84286011-G-Achr9-84286011-G-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

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

2

Clinical Significance

Benign criteria provided, single submitter B:1

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

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.773 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
SLC28A3NM_001199633.2 linkuse as main transcriptc.1381C>T p.Leu461= synonymous_variant 13/18 ENST00000376238.5
SLC28A3-AS1XR_001746802.1 linkuse as main transcriptn.231-3929G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC28A3ENST00000376238.5 linkuse as main transcriptc.1381C>T p.Leu461= synonymous_variant 13/181 NM_001199633.2 P1Q9HAS3-1
SLC28A3-AS1ENST00000419815.1 linkuse as main transcriptn.182-3929G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.187
AC:
28410
AN:
152030
Hom.:
3136
Cov.:
32
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.:
33
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.187
AC:
28460
AN:
152148
Hom.:
3142
Cov.:
32
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:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJul 15, 2019- -

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.

Other links and lift over

dbSNP: rs7853758; hg19: chr9-86900926; COSMIC: COSV66153362; API