dbSNP rs2096525: MIF-AS1:n.1270A>G (chr22-23894632-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000406213.1(MIF-AS1):n.1270A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 1,488,392 control chromosomes in the GnomAD database, including 26,303 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 0.20 ( 3133 hom., cov: 31)

Exomes 𝑓: 0.19 ( 23170 hom. )

Consequence

MIF-AS1
ENST00000406213.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.95

Publications

30 publications found

Variant links:

Genes affected

MIF-AS1 (HGNC:27669): (MIF antisense RNA 1)

MIF-AS1 links:

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

MIF links:

ENSG00000251357 (HGNC:):

ENSG00000251357 links:

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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIF	NM_002415.2 link	c.108+50T>C		intron_variant	Intron 1 of 2	ENST00000215754.8	NP_002406.1
MIF-AS1	NR_038911.1 link	n.1270A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIF	ENST00000215754.8 link	c.108+50T>C		intron_variant	Intron 1 of 2	1	NM_002415.2	ENSP00000215754.7
ENSG00000251357	ENST00000433835.3 link	c.432-140T>C		intron_variant	Intron 4 of 5	5		ENSP00000400325.3

Frequencies

GnomAD3 genomes

AF:

0.204

AC:

29894

AN:

146614

Hom.:

3125

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.240

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.249

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.185

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.184

GnomAD2 exomes

AF:

0.203

AC:

43115

AN:

212084

AF XY:

0.201

show subpopulations

Gnomad AFR exome

AF:

0.221

Gnomad AMR exome

AF:

0.283

Gnomad ASJ exome

AF:

0.139

Gnomad EAS exome

AF:

0.196

Gnomad FIN exome

AF:

0.236

Gnomad NFE exome

AF:

0.169

Gnomad OTH exome

AF:

0.194

GnomAD4 exome

AF:

0.187

AC:

251191

AN:

1341642

Hom.:

23170

Cov.:

AF XY:

0.188

AC XY:

125602

AN XY:

669646

show subpopulations

African (AFR)

AF:

0.230

AC:

7139

AN:

31082

American (AMR)

AF:

0.278

AC:

11399

AN:

41060

Ashkenazi Jewish (ASJ)

AF:

0.152

AC:

3540

AN:

23334

East Asian (EAS)

AF:

0.205

AC:

7130

AN:

34712

South Asian (SAS)

AF:

0.229

AC:

19064

AN:

83366

European-Finnish (FIN)

AF:

0.243

AC:

10885

AN:

44862

Middle Eastern (MID)

AF:

0.170

AC:

763

AN:

4484

European-Non Finnish (NFE)

AF:

0.176

AC:

180693

AN:

1023990

Other (OTH)

AF:

0.193

AC:

10578

AN:

54752

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

11311

22622

33934

45245

56556

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6606

13212

19818

26424

33030

<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:

0.204

AC:

29928

AN:

146750

Hom.:

3133

Cov.:

AF XY:

0.209

AC XY:

14958

AN XY:

71494

show subpopulations

African (AFR)

AF:

0.229

AC:

9283

AN:

40528

American (AMR)

AF:

0.241

AC:

3587

AN:

14890

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

458

AN:

3416

East Asian (EAS)

AF:

0.207

AC:

943

AN:

4550

South Asian (SAS)

AF:

0.250

AC:

1084

AN:

4344

European-Finnish (FIN)

AF:

0.248

AC:

2389

AN:

9628

Middle Eastern (MID)

AF:

0.178

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.175

AC:

11589

AN:

66152

Other (OTH)

AF:

0.181

AC:

374

AN:

2066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

1201

2403

3604

4806

6007

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<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:

0.182

Hom.:

533

Bravo

AF:

0.196

Asia WGS

AF:

0.224

AC:

779

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.2

(source)

DANN

Benign

0.50

PhyloP100

-1.9

PromoterAI

-0.092

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over