Genetic Variant MIF-AS1:n.17G>A (chr22-23898914-C-T) – 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.17G>A 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 0.461 in 152,062 control chromosomes in the GnomAD database, including 17,657 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 0.46 ( 17653 hom., cov: 32)

Exomes 𝑓: 0.58 ( 4 hom. )

Consequence

MIF-AS1
ENST00000406213.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.94

Publications

55 publications found

Variant links:

COSMIC-nc: COSV53158774

Genes affected

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

MIF-AS1 links:

ENSG00000290199 (HGNC:):

ENSG00000290199 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=-1.02).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000406213.1. 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.17G>A		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIF-AS1	ENST00000406213.1	TSL:1	n.17G>A	non_coding_transcript_exon	Exon 1 of 3
ENSG00000290199	ENST00000703580.1		n.387-2804G>A	intron	N/A
ENSG00000290199	ENST00000717616.1		n.213-7448G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.461

AC:

70102

AN:

151920

Hom.:

17640

Cov.:

show subpopulations

Gnomad AFR

AF:

0.247

Gnomad AMI

AF:

0.607

Gnomad AMR

AF:

0.508

Gnomad ASJ

AF:

0.468

Gnomad EAS

AF:

0.465

Gnomad SAS

AF:

0.621

Gnomad FIN

AF:

0.613

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.544

Gnomad OTH

AF:

0.463

GnomAD4 exome

AF:

0.583

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.461

AC:

70126

AN:

152038

Hom.:

17653

Cov.:

AF XY:

0.470

AC XY:

34932

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.246

AC:

10214

AN:

41450

American (AMR)

AF:

0.509

AC:

7774

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.468

AC:

1623

AN:

3470

East Asian (EAS)

AF:

0.464

AC:

2394

AN:

5154

South Asian (SAS)

AF:

0.622

AC:

2999

AN:

4818

European-Finnish (FIN)

AF:

0.613

AC:

6477

AN:

10564

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.544

AC:

36974

AN:

67978

Other (OTH)

AF:

0.464

AC:

980

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1822

3644

5466

7288

9110

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

648

1296

1944

2592

3240

<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:

0.517

Hom.:

90597

Bravo

AF:

0.443

Asia WGS

AF:

0.526

AC:

1831

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.21

(source)

DANN

Benign

0.68

PhyloP100

-2.9

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over