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GeneBe

15-84905565-A-T

Variant summary

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

The NM_004213.5(SLC28A1):c.630A>T(p.Gly210=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00524 in 1,613,586 control chromosomes in the GnomAD database, including 365 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.028 ( 200 hom., cov: 33)
Exomes 𝑓: 0.0029 ( 165 hom. )

Consequence

SLC28A1
NM_004213.5 synonymous

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -0.381
Variant links:
Genes affected
SLC28A1 (HGNC:11001): (solute carrier family 28 member 1) Enables azole transmembrane transporter activity; cytidine transmembrane transporter activity; and uridine transmembrane transporter activity. Involved in azole transmembrane transport; nucleoside transport; and pyrimidine-containing compound transmembrane transport. Located in cytosol; nuclear speck; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 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=-0.67).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 15-84905565-A-T is Benign according to our data. Variant chr15-84905565-A-T is described in ClinVar as [Benign]. Clinvar id is 780006.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 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=-0.381 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 = 0.092 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC28A1NM_004213.5 linkuse as main transcriptc.630A>T p.Gly210= synonymous_variant 8/19 ENST00000394573.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC28A1ENST00000394573.6 linkuse as main transcriptc.630A>T p.Gly210= synonymous_variant 8/191 NM_004213.5 P1O00337-1
SLC28A1ENST00000286749.3 linkuse as main transcriptc.630A>T p.Gly210= synonymous_variant 7/181 P1O00337-1
SLC28A1ENST00000538177.5 linkuse as main transcriptc.630A>T p.Gly210= synonymous_variant 7/152

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0277
AC:
4211
AN:
151978
Hom.:
199
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0947
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0143
Gnomad ASJ
AF:
0.00403
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.0230
GnomAD3 exomes
AF:
0.00743
AC:
1869
AN:
251454
Hom.:
74
AF XY:
0.00527
AC XY:
716
AN XY:
135910
show subpopulations
Gnomad AFR exome
AF:
0.0984
Gnomad AMR exome
AF:
0.00506
Gnomad ASJ exome
AF:
0.00367
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000163
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000211
Gnomad OTH exome
AF:
0.00456
GnomAD4 exome
AF:
0.00290
AC:
4245
AN:
1461490
Hom.:
165
Cov.:
31
AF XY:
0.00248
AC XY:
1804
AN XY:
727078
show subpopulations
Gnomad4 AFR exome
AF:
0.0964
Gnomad4 AMR exome
AF:
0.00639
Gnomad4 ASJ exome
AF:
0.00406
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000278
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.000152
Gnomad4 OTH exome
AF:
0.00697
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0277
AC:
4211
AN:
152096
Hom.:
200
Cov.:
33
AF XY:
0.0269
AC XY:
2000
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.0944
Gnomad4 AMR
AF:
0.0143
Gnomad4 ASJ
AF:
0.00403
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.0228
Alfa
AF:
0.00828
Hom.:
13
Bravo
AF:
0.0317
Asia WGS
AF:
0.00375
AC:
13
AN:
3478
EpiCase
AF:
0.000164
EpiControl
AF:
0.000296

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeApr 10, 2018- -
SLC28A1-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesNov 26, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
Cadd
Benign
9.2
Dann
Benign
0.67

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs8187755; hg19: chr15-85448796; API