rs885004

Variant summary

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

The NM_001199633.2(SLC28A3):​c.862-360C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,208 control chromosomes in the GnomAD database, including 1,138 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 0.12 ( 1138 hom., cov: 32)

Consequence

SLC28A3
NM_001199633.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.967
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]

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 (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC28A3NM_001199633.2 linkuse as main transcriptc.862-360C>T intron_variant ENST00000376238.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC28A3ENST00000376238.5 linkuse as main transcriptc.862-360C>T intron_variant 1 NM_001199633.2 P1Q9HAS3-1

Frequencies

GnomAD3 genomes
AF:
0.119
AC:
18116
AN:
152090
Hom.:
1134
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.102
Gnomad AMI
AF:
0.0581
Gnomad AMR
AF:
0.153
Gnomad ASJ
AF:
0.214
Gnomad EAS
AF:
0.149
Gnomad SAS
AF:
0.120
Gnomad FIN
AF:
0.0539
Gnomad MID
AF:
0.117
Gnomad NFE
AF:
0.125
Gnomad OTH
AF:
0.144
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.119
AC:
18142
AN:
152208
Hom.:
1138
Cov.:
32
AF XY:
0.115
AC XY:
8591
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.102
Gnomad4 AMR
AF:
0.154
Gnomad4 ASJ
AF:
0.214
Gnomad4 EAS
AF:
0.148
Gnomad4 SAS
AF:
0.121
Gnomad4 FIN
AF:
0.0539
Gnomad4 NFE
AF:
0.125
Gnomad4 OTH
AF:
0.143
Alfa
AF:
0.132
Hom.:
1971
Bravo
AF:
0.126
Asia WGS
AF:
0.149
AC:
519
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
5.5
DANN
Benign
0.29

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: rs885004; hg19: chr9-86909550; API