rs9282783

Variant names:

• chr22-23894172-C-G
• rs9282783
• ENST00000433835.3:c.432-600C>G

Your query was ambiguous. Multiple possible variants found:

• chr22-23894172-C-G
• chr22-23894172-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 8 publications found

Genes affected

ENSG00000251357 (HGNC:):

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433835.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIF-AS1	NR_038911.1		n.1730G>C		non_coding_transcript_exon	Exon 3 of 3
	MIF	NM_002415.2	MANE Select	c.-303C>G		upstream_gene	N/A	NP_002406.1	P14174

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251357	ENST00000433835.3	TSL:5	c.432-600C>G		intron	N/A	ENSP00000400325.3	H7C1H1
	ENSG00000290199	ENST00000717616.1		n.213-2706G>C		intron	N/A
	MIF	ENST00000215754.8	TSL:1 MANE Select	c.-303C>G		upstream_gene	N/A	ENSP00000215754.7	P14174

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4139 AN: 152290 Hom.: 162 Cov.: 33

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

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

GnomAD4 genome AF: 0.0273 AC: 4161 AN: 152408 Hom.: 167 Cov.: 33 AF XY: 0.0268 AC XY: 1999 AN XY: 74532

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

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9282783;

hg19: chr22-24236359;