6-44221578-T-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The ENST00000393844.7(SLC29A1):c.-52+1796T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000054 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC29A1
ENST00000393844.7 intron
ENST00000393844.7 intron
Scores
2
Splicing: ADA: 0.0002345
2
Clinical Significance
Conservation
PhyloP100: 0.196
Genes affected
SLC29A1 (HGNC:11003): (solute carrier family 29 member 1 (Augustine blood group)) This gene is a member of the equilibrative nucleoside transporter family. The gene encodes a transmembrane glycoprotein that localizes to the plasma and mitochondrial membranes and mediates the cellular uptake of nucleosides from the surrounding medium. The protein is categorized as an equilibrative (as opposed to concentrative) transporter that is sensitive to inhibition by nitrobenzylthioinosine (NBMPR). Nucleoside transporters are required for nucleotide synthesis in cells that lack de novo nucleoside synthesis pathways, and are also necessary for the uptake of cytotoxic nucleosides used for cancer and viral chemotherapies. Multiple alternatively spliced variants, encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 6-44221578-T-A is Benign according to our data. Variant chr6-44221578-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 3044005.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC29A1 | NM_001304462.2 | c.87-8T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_001291391.1 | ||||
SLC29A1 | NM_001304465.2 | c.24+1796T>A | intron_variant | NP_001291394.1 | ||||
SLC29A1 | NM_001304466.2 | c.24+1796T>A | intron_variant | NP_001291395.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC29A1 | ENST00000393844.7 | c.-52+1796T>A | intron_variant | 1 | ENSP00000377427 | P1 | ||||
SLC29A1 | ENST00000371713.6 | c.-151-8T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | ENSP00000360778 | P1 | ||||
SLC29A1 | ENST00000643028.2 | c.-29+1796T>A | intron_variant | ENSP00000495211 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 8AN: 148100Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00123 AC: 890AN: 722554Hom.: 0 Cov.: 15 AF XY: 0.00116 AC XY: 427AN XY: 367156
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000540 AC: 8AN: 148232Hom.: 0 Cov.: 32 AF XY: 0.0000553 AC XY: 4AN XY: 72382
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SLC29A1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 01, 2023 | 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
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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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
Publications
No publications associated with this variant yet.