rs767558450

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001370592.1(MIF4GD):​c.298G>T​(p.Gly100Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000547 in 1,461,692 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. G100R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000055 ( 0 hom. )

Consequence

MIF4GD
NM_001370592.1 missense

Scores

1
5
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.67
Variant links:
Genes affected
MIF4GD (HGNC:24030): (MIF4G domain containing) This gene encodes a protein which interacts with the N-terminus of the stem-loop binding protein (SLBP) and the 3' end of histone mRNA. This interaction facilitates the activation of histone mRNA translation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jun 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MIF4GDNM_001370592.1 linkc.298G>T p.Gly100Cys missense_variant Exon 4 of 6 ENST00000325102.13 NP_001357521.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIF4GDENST00000325102.13 linkc.298G>T p.Gly100Cys missense_variant Exon 4 of 6 2 NM_001370592.1 ENSP00000321625.8 A9UHW6-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251030
Hom.:
0
AF XY:
0.00000737
AC XY:
1
AN XY:
135716
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000881
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000547
AC:
8
AN:
1461692
Hom.:
0
Cov.:
32
AF XY:
0.00000688
AC XY:
5
AN XY:
727156
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:
0.00000719
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
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.069
T
BayesDel_noAF
Benign
-0.34
CADD
Pathogenic
26
DANN
Benign
0.96
DEOGEN2
Benign
0.054
T;T;.;.;.;.;.;T;T
Eigen
Uncertain
0.60
Eigen_PC
Uncertain
0.65
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.92
.;D;D;.;D;D;D;D;D
M_CAP
Benign
0.022
T
MetaRNN
Uncertain
0.48
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.69
N;N;.;.;.;.;.;.;.
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-2.2
N;.;N;.;.;.;.;.;.
REVEL
Benign
0.29
Sift
Benign
0.037
D;.;D;.;.;.;.;.;.
Sift4G
Benign
0.080
T;T;T;T;T;.;T;.;.
Polyphen
0.93
P;P;D;.;.;.;.;.;.
Vest4
0.55
MutPred
0.59
Loss of MoRF binding (P = 0.082);Loss of MoRF binding (P = 0.082);.;.;.;.;Loss of MoRF binding (P = 0.082);Loss of MoRF binding (P = 0.082);.;
MVP
0.55
MPC
0.81
ClinPred
0.94
D
GERP RS
5.6
Varity_R
0.32
gMVP
0.28

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.10
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs767558450; hg19: chr17-73263877; API