18-673995-T-G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017512.7(ENOSF1):c.*310A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000145 in 207,496 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000018 ( 0 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: 0.128
Publications
13 publications found
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_017512.7. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ENOSF1 | MANE Select | c.*310A>C | 3_prime_UTR | Exon 16 of 16 | ENSP00000497230.2 | Q7L5Y1-1 | |||
| ENOSF1 | TSL:1 | c.*144+166A>C | intron | N/A | ENSP00000373072.3 | Q7L5Y1-2 | |||
| ENOSF1 | TSL:1 | n.*1029A>C | non_coding_transcript_exon | Exon 14 of 14 | ENSP00000464614.1 | J3QSB6 |
Frequencies
GnomAD3 genomes 0.0000132 AC: 2AN: 151836Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
151836
Hom.:
Cov.:
31
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:
GnomAD4 exome AF: 0.0000180 AC: 1AN: 55660Hom.: 0 Cov.: 0 AF XY: 0.0000352 AC XY: 1AN XY: 28392 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
55660
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
28392
show subpopulations
African (AFR)
AF:
AC:
0
AN:
1740
American (AMR)
AF:
AC:
0
AN:
1990
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
1984
East Asian (EAS)
AF:
AC:
0
AN:
3012
South Asian (SAS)
AF:
AC:
0
AN:
3396
European-Finnish (FIN)
AF:
AC:
0
AN:
2672
Middle Eastern (MID)
AF:
AC:
0
AN:
272
European-Non Finnish (NFE)
AF:
AC:
0
AN:
36802
Other (OTH)
AF:
AC:
1
AN:
3792
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000132 AC: 2AN: 151836Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74146 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
151836
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
74146
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41274
American (AMR)
AF:
AC:
0
AN:
15238
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5180
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10548
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67986
Other (OTH)
AF:
AC:
0
AN:
2088
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.650
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.