rs199562010

Variant summary

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

The NM_175902.5(OGFOD3):​c.851G>T​(p.Cys284Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,460 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 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. C284Y) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

OGFOD3
NM_175902.5 missense

Scores

1
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0200
Variant links:
Genes affected
OGFOD3 (HGNC:26174): (2-oxoglutarate and iron dependent oxygenase domain containing 3) Predicted to enable several functions, including L-ascorbic acid binding activity; dioxygenase activity; and iron ion binding activity. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.11637476).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OGFOD3NM_024648.3 linkc.824-1982G>T intron_variant Intron 8 of 8 ENST00000313056.10 NP_078924.1 Q6PK18-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OGFOD3ENST00000313056.10 linkc.824-1982G>T intron_variant Intron 8 of 8 2 NM_024648.3 ENSP00000320116.5 Q6PK18-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1460460
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
726580
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.65
CADD
Benign
2.5
DANN
Benign
0.89
Eigen
Benign
-0.77
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.061
N
LIST_S2
Benign
0.23
T
M_CAP
Benign
0.0016
T
MetaRNN
Benign
0.12
T
MetaSVM
Benign
-1.0
T
PROVEAN
Benign
0.21
N
REVEL
Benign
0.015
Sift
Benign
0.039
D
Sift4G
Uncertain
0.016
D
Polyphen
0.80
P
Vest4
0.25
MutPred
0.28
Loss of catalytic residue at M282 (P = 7e-04);
MVP
0.20
MPC
0.17
ClinPred
0.90
D
GERP RS
-0.21
gMVP
0.44

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: chr17-80352392; API