rs7853758
Positions:
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
NM_001199633.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.773
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 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_single_submitter, 1 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 | UniProt |
---|---|---|---|---|---|---|---|
SLC28A3 | NM_001199633.2 | c.1381C>T | p.Leu461= | synonymous_variant | 13/18 | ENST00000376238.5 | |
SLC28A3-AS1 | XR_001746802.1 | n.231-3929G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC28A3 | ENST00000376238.5 | c.1381C>T | p.Leu461= | synonymous_variant | 13/18 | 1 | NM_001199633.2 | P1 | |
SLC28A3-AS1 | ENST00000419815.1 | n.182-3929G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.187 AC: 28410AN: 152030Hom.: 3136 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
28410
AN:
152030
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.153 AC: 38437AN: 250790Hom.: 3336 AF XY: 0.147 AC XY: 19910AN XY: 135514
GnomAD3 exomes
AF:
AC:
38437
AN:
250790
Hom.:
AF XY:
AC XY:
19910
AN XY:
135514
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.145 AC: 211832AN: 1461532Hom.: 16505 Cov.: 33 AF XY: 0.144 AC XY: 104536AN XY: 727050
GnomAD4 exome
AF:
AC:
211832
AN:
1461532
Hom.:
Cov.:
33
AF XY:
AC XY:
104536
AN XY:
727050
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.187 AC: 28460AN: 152148Hom.: 3142 Cov.: 32 AF XY: 0.180 AC XY: 13410AN XY: 74412
GnomAD4 genome
?
AF:
AC:
28460
AN:
152148
Hom.:
Cov.:
32
AF XY:
AC XY:
13410
AN XY:
74412
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
568
AN:
3478
EpiCase
AF:
EpiControl
AF:
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 submitter | clinical testing | GeneDx | Jul 15, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at