rs3826626
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017512.7(ENOSF1):c.*3417A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0206 in 1,612,726 control chromosomes in the GnomAD database, including 2,427 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 0.067 ( 830 hom., cov: 32)
Exomes 𝑓: 0.016 ( 1597 hom. )
Consequence
ENOSF1
NM_017512.7 3_prime_UTR
NM_017512.7 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.700
Genes affected
ENOSF1 (HGNC:30365): (enolase superfamily member 1) This gene can encode a mitochondrial enzyme that is thought to convert L-fuconate to 2-keto-3-deoxy-L-fuconate. This locus was originally identified as the source of antisense RNAs of the adjacent thymidylate synthase gene. Splice variants at this locus may contain an alternate 3' exon that is complementary to the 3'UTR and terminal intron of the thymidylate synthase (TS) RNA and may downregulate TS expression. [provided by RefSeq, Aug 2017]
TYMS (HGNC:12441): (thymidylate synthetase) Thymidylate synthase catalyzes the methylation of deoxyuridylate to deoxythymidylate using, 10-methylenetetrahydrofolate (methylene-THF) as a cofactor. This function maintains the dTMP (thymidine-5-prime monophosphate) pool critical for DNA replication and repair. The enzyme has been of interest as a target for cancer chemotherapeutic agents. It is considered to be the primary site of action for 5-fluorouracil, 5-fluoro-2-prime-deoxyuridine, and some folate analogs. Expression of this gene and that of a naturally occurring antisense transcript, mitochondrial enolase superfamily member 1 (GeneID:55556), vary inversely when cell-growth progresses from late-log to plateau phase. Polymorphisms in this gene may be associated with etiology of neoplasia, including breast cancer, and response to chemotherapy. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENOSF1 | NM_017512.7 | c.*3417A>G | 3_prime_UTR_variant | 16/16 | ENST00000647584.2 | ||
TYMS | NM_001071.4 | c.732+21T>C | intron_variant | ENST00000323274.15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENOSF1 | ENST00000647584.2 | c.*3417A>G | 3_prime_UTR_variant | 16/16 | NM_017512.7 | P1 | |||
TYMS | ENST00000323274.15 | c.732+21T>C | intron_variant | 1 | NM_001071.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0669 AC: 10169AN: 151998Hom.: 827 Cov.: 32
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GnomAD3 exomes AF: 0.0447 AC: 11143AN: 249496Hom.: 922 AF XY: 0.0384 AC XY: 5171AN XY: 134772
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GnomAD4 exome AF: 0.0158 AC: 23053AN: 1460610Hom.: 1597 Cov.: 31 AF XY: 0.0147 AC XY: 10708AN XY: 726534
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GnomAD4 genome ? AF: 0.0670 AC: 10194AN: 152116Hom.: 830 Cov.: 32 AF XY: 0.0697 AC XY: 5182AN XY: 74348
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ClinVar
Not reported inComputational 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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at