15-84888762-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_004213.5(SLC28A1):c.97-10C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.001 in 1,549,480 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0051 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00056 ( 6 hom. )
Consequence
SLC28A1
NM_004213.5 splice_polypyrimidine_tract, intron
NM_004213.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00004090
2
Clinical Significance
Conservation
PhyloP100: -0.254
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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 15-84888762-C-T is Benign according to our data. Variant chr15-84888762-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3056473.Status of the report is no_assertion_criteria_provided, 0 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00506 (770/152314) while in subpopulation AFR AF= 0.0173 (719/41558). AF 95% confidence interval is 0.0163. There are 5 homozygotes in gnomad4. There are 361 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC28A1 | NM_004213.5 | c.97-10C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000394573.6 | NP_004204.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC28A1 | ENST00000394573.6 | c.97-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004213.5 | ENSP00000378074 | P1 | |||
SLC28A1 | ENST00000286749.3 | c.97-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000286749 | P1 | ||||
SLC28A1 | ENST00000338602.6 | c.97-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000341629 | |||||
SLC28A1 | ENST00000538177.5 | c.97-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 2 | ENSP00000443752 |
Frequencies
GnomAD3 genomes AF: 0.00503 AC: 766AN: 152196Hom.: 5 Cov.: 32
GnomAD3 genomes
AF:
AC:
766
AN:
152196
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: 0.00136 AC: 210AN: 154606Hom.: 2 AF XY: 0.000953 AC XY: 78AN XY: 81874
GnomAD3 exomes
AF:
AC:
210
AN:
154606
Hom.:
AF XY:
AC XY:
78
AN XY:
81874
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: 0.000560 AC: 783AN: 1397166Hom.: 6 Cov.: 30 AF XY: 0.000453 AC XY: 312AN XY: 689408
GnomAD4 exome
AF:
AC:
783
AN:
1397166
Hom.:
Cov.:
30
AF XY:
AC XY:
312
AN XY:
689408
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: 0.00506 AC: 770AN: 152314Hom.: 5 Cov.: 32 AF XY: 0.00485 AC XY: 361AN XY: 74472
GnomAD4 genome
AF:
AC:
770
AN:
152314
Hom.:
Cov.:
32
AF XY:
AC XY:
361
AN XY:
74472
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:
2
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SLC28A1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 26, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at