rs58085394
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_017512.7(ENOSF1):c.105G>A(p.Ser35=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 1,612,488 control chromosomes in the GnomAD database, including 15,140 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 0.11 ( 1085 hom., cov: 31)
Exomes 𝑓: 0.13 ( 14055 hom. )
Consequence
ENOSF1
NM_017512.7 synonymous
NM_017512.7 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.17
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP7
?
Synonymous conserved (PhyloP=-1.17 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENOSF1 | NM_017512.7 | c.105G>A | p.Ser35= | synonymous_variant | 2/16 | ENST00000647584.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENOSF1 | ENST00000647584.2 | c.105G>A | p.Ser35= | synonymous_variant | 2/16 | NM_017512.7 | P1 | ||
ENST00000580007.1 | n.36C>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.107 AC: 16192AN: 151756Hom.: 1087 Cov.: 31
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GnomAD3 exomes AF: 0.125 AC: 31442AN: 251422Hom.: 2433 AF XY: 0.124 AC XY: 16914AN XY: 135888
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GnomAD4 exome AF: 0.134 AC: 195193AN: 1460616Hom.: 14055 Cov.: 31 AF XY: 0.132 AC XY: 95829AN XY: 726704
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GnomAD4 genome ? AF: 0.107 AC: 16182AN: 151872Hom.: 1085 Cov.: 31 AF XY: 0.106 AC XY: 7846AN XY: 74182
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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
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at