rs2612086

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_017512.7(ENOSF1):​c.434T>G​(p.Met145Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M145T) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

ENOSF1
NM_017512.7 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0220
Variant links:
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.10867289).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ENOSF1NM_017512.7 linkc.434T>G p.Met145Arg missense_variant Exon 6 of 16 ENST00000647584.2 NP_059982.2 Q7L5Y1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENOSF1ENST00000647584.2 linkc.434T>G p.Met145Arg missense_variant Exon 6 of 16 NM_017512.7 ENSP00000497230.2 Q7L5Y1-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
35
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.065
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.58
CADD
Benign
0.18
DANN
Benign
0.92
DEOGEN2
Benign
0.043
.;.;T;.;.
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.35
N
LIST_S2
Benign
0.84
T;T;T;T;T
M_CAP
Benign
0.0077
T
MetaRNN
Benign
0.11
T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
-0.12
.;.;N;.;.
PrimateAI
Benign
0.31
T
PROVEAN
Benign
1.1
.;N;N;.;.
REVEL
Benign
0.033
Sift
Uncertain
0.013
.;D;D;.;.
Sift4G
Uncertain
0.047
.;D;T;.;T
Polyphen
0.0
.;B;B;.;.
Vest4
0.11, 0.11
MutPred
0.59
.;.;Loss of stability (P = 0.0777);.;.;
MVP
0.014
MPC
0.014
ClinPred
0.26
T
GERP RS
-1.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.15

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-691266; API