Genetic Variant MIAT:n.4787G>T (chr22-26671261-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000613780.4(MIAT):n.4929G>T 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 0.425 in 398,356 control chromosomes in the GnomAD database, including 37,676 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 0.39 ( 12382 hom., cov: 31)

Exomes 𝑓: 0.45 ( 25294 hom. )

Consequence

MIAT
ENST00000613780.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0130

Publications

31 publications found

Variant links:

COSMIC-nc: COSV66896792

Genes affected

MIAT (HGNC:33425): (myocardial infarction associated transcript) This gene encodes a spliced long non-coding RNA that may constitute a component of the nuclear matrix. Altered expression of this locus has been reported to be associated with a susceptibility to myocardial infarction. It has also been proposed that pathways involving this transcript may contribute to the pathophysiology of schizophrenia. A similar gene in mouse has been associated with retinal cell fate determination. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Dec 2014]

MIAT links:

ENSG00000206028 (HGNC:):

ENSG00000206028 links:

MIATNB (HGNC:50731): (MIAT neighbor)

MIATNB 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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000613780.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIAT	NR_033320.3	MANE Select	n.4787G>T	non_coding_transcript_exon	Exon 5 of 5
MIAT	NR_003491.4		n.4861G>T	non_coding_transcript_exon	Exon 5 of 5
MIAT	NR_033319.3		n.4735G>T	non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIAT	ENST00000620145.6	TSL:1 MANE Select	n.4787G>T	non_coding_transcript_exon	Exon 5 of 5
MIAT	ENST00000613780.4	TSL:1	n.4929G>T	non_coding_transcript_exon	Exon 5 of 5
MIAT	ENST00000616213.4	TSL:1	n.4729G>T	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58673

AN:

151866

Hom.:

12369

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.395

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.490

Gnomad FIN

AF:

0.488

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.461

Gnomad OTH

AF:

0.419

GnomAD4 exome

AF:

0.449

AC:

110579

AN:

246372

Hom.:

25294

Cov.:

AF XY:

0.451

AC XY:

56282

AN XY:

124848

show subpopulations

African (AFR)

AF:

0.221

AC:

1586

AN:

7182

American (AMR)

AF:

0.407

AC:

3025

AN:

7434

Ashkenazi Jewish (ASJ)

AF:

0.456

AC:

4215

AN:

9240

East Asian (EAS)

AF:

0.415

AC:

9511

AN:

22896

South Asian (SAS)

AF:

0.503

AC:

1525

AN:

3030

European-Finnish (FIN)

AF:

0.488

AC:

10157

AN:

20828

Middle Eastern (MID)

AF:

0.401

AC:

519

AN:

1294

European-Non Finnish (NFE)

AF:

0.462

AC:

73060

AN:

158094

Other (OTH)

AF:

0.426

AC:

6981

AN:

16374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

4434

8868

13301

17735

22169

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

310

620

930

1240

1550

<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:

0.386

AC:

58724

AN:

151984

Hom.:

12382

Cov.:

AF XY:

0.389

AC XY:

28898

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.216

AC:

8970

AN:

41476

American (AMR)

AF:

0.395

AC:

6041

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.447

AC:

1552

AN:

3472

East Asian (EAS)

AF:

0.384

AC:

1984

AN:

5162

South Asian (SAS)

AF:

0.489

AC:

2355

AN:

4814

European-Finnish (FIN)

AF:

0.488

AC:

5151

AN:

10556

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.461

AC:

31302

AN:

67910

Other (OTH)

AF:

0.425

AC:

895

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1733

3467

5200

6934

8667

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

558

1116

1674

2232

2790

<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:

0.427

Hom.:

3010

Bravo

AF:

0.369

Asia WGS

AF:

0.458

AC:

1594

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.9

(source)

DANN

Benign

0.47

PhyloP100

0.013

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