22-23894172-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000433835.3(ENSG00000251357):​c.432-600C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 539,296 control chromosomes in the GnomAD database, including 229 homozygotes. 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 0.027 ( 167 hom., cov: 33)
Exomes 𝑓: 0.0062 ( 62 hom. )

Consequence

ENSG00000251357
ENST00000433835.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00

Publications

8 publications found
Variant links:
Genes affected
MIF-AS1 (HGNC:27669): (MIF antisense RNA 1)
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 Gene-Disease associations (from GenCC):
  • cystic fibrosis
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MIF-AS1NR_038911.1 linkn.1730G>C non_coding_transcript_exon_variant Exon 3 of 3
MIFNM_002415.2 linkc.-303C>G upstream_gene_variant ENST00000215754.8 NP_002406.1 P14174I4AY87

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000251357ENST00000433835.3 linkc.432-600C>G intron_variant Intron 4 of 5 5 ENSP00000400325.3 H7C1H1
ENSG00000290199ENST00000717616.1 linkn.213-2706G>C intron_variant Intron 2 of 2
MIFENST00000215754.8 linkc.-303C>G upstream_gene_variant 1 NM_002415.2 ENSP00000215754.7 P14174

Frequencies

GnomAD3 genomes
AF:
0.0272
AC:
4139
AN:
152290
Hom.:
162
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0898
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0126
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.0302
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000411
Gnomad OTH
AF:
0.0205
GnomAD4 exome
AF:
0.00618
AC:
2392
AN:
386888
Hom.:
62
Cov.:
0
AF XY:
0.00747
AC XY:
1531
AN XY:
205058
show subpopulations
African (AFR)
AF:
0.0848
AC:
625
AN:
7374
American (AMR)
AF:
0.0107
AC:
140
AN:
13104
Ashkenazi Jewish (ASJ)
AF:
0.00131
AC:
15
AN:
11444
East Asian (EAS)
AF:
0.00
AC:
0
AN:
24258
South Asian (SAS)
AF:
0.0305
AC:
1277
AN:
41904
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
27122
Middle Eastern (MID)
AF:
0.00413
AC:
7
AN:
1696
European-Non Finnish (NFE)
AF:
0.000358
AC:
85
AN:
237416
Other (OTH)
AF:
0.0108
AC:
243
AN:
22570
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.491
Heterozygous variant carriers
0
111
222
332
443
554
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0273
AC:
4161
AN:
152408
Hom.:
167
Cov.:
33
AF XY:
0.0268
AC XY:
1999
AN XY:
74532
show subpopulations
African (AFR)
AF:
0.0900
AC:
3746
AN:
41600
American (AMR)
AF:
0.0125
AC:
192
AN:
15314
Ashkenazi Jewish (ASJ)
AF:
0.000864
AC:
3
AN:
3472
East Asian (EAS)
AF:
0.000193
AC:
1
AN:
5192
South Asian (SAS)
AF:
0.0302
AC:
146
AN:
4834
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10628
Middle Eastern (MID)
AF:
0.00680
AC:
2
AN:
294
European-Non Finnish (NFE)
AF:
0.000411
AC:
28
AN:
68046
Other (OTH)
AF:
0.0203
AC:
43
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
215
430
645
860
1075
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
42
84
126
168
210
<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:
0.0162
Hom.:
12
Bravo
AF:
0.0310
Asia WGS
AF:
0.0190
AC:
66
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.78
DANN
Benign
0.52
PhyloP100
-2.0
PromoterAI
0.42
Neutral
Mutation Taster
=300/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs9282783; hg19: chr22-24236359; API