rs1049829

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The ENST00000215754.8(MIF):​c.175C>T​(p.Leu59Phe) 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 pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

MIF
ENST00000215754.8 missense

Scores

2
7
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.39
Variant links:
Genes affected
MIF (HGNC:7097): (macrophage migration inhibitory factor) This gene encodes a lymphokine involved in cell-mediated immunity, immunoregulation, and inflammation. It plays a role in the regulation of macrophage function in host defense through the suppression of anti-inflammatory effects of glucocorticoids. This lymphokine and the JAB1 protein form a complex in the cytosol near the peripheral plasma membrane, which may indicate an additional role in integrin signaling pathways. [provided by RefSeq, Jul 2008]
MIF-AS1 (HGNC:27669): (MIF antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.754

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MIFNM_002415.2 linkuse as main transcriptc.175C>T p.Leu59Phe missense_variant 2/3 ENST00000215754.8 NP_002406.1
MIF-AS1NR_038911.1 linkuse as main transcriptn.1064G>A non_coding_transcript_exon_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MIFENST00000215754.8 linkuse as main transcriptc.175C>T p.Leu59Phe missense_variant 2/31 NM_002415.2 ENSP00000215754 P1
MIF-AS1ENST00000406213.1 linkuse as main transcriptn.1064G>A non_coding_transcript_exon_variant 3/31
MIFENST00000465752.1 linkuse as main transcriptn.200C>T non_coding_transcript_exon_variant 2/21
MIFENST00000498385.1 linkuse as main transcriptn.141C>T non_coding_transcript_exon_variant 1/22

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.33
BayesDel_addAF
Uncertain
0.048
T
BayesDel_noAF
Benign
-0.17
CADD
Pathogenic
26
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.45
T
Eigen
Uncertain
0.47
Eigen_PC
Uncertain
0.49
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.69
T
M_CAP
Benign
0.0092
T
MetaRNN
Pathogenic
0.75
D
MetaSVM
Benign
-0.74
T
MutationAssessor
Benign
1.7
L
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.77
T
PROVEAN
Benign
-2.2
N
REVEL
Uncertain
0.40
Sift
Benign
0.054
T
Sift4G
Benign
0.34
T
Polyphen
1.0
D
Vest4
0.67
MutPred
0.63
Gain of sheet (P = 0.0827);
MVP
0.36
MPC
1.3
ClinPred
0.91
D
GERP RS
5.0
Varity_R
0.50
gMVP
0.75

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1049829; hg19: chr22-24237025; API