Genetic Variant MIAT:n.4929G>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

29 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIAT	NR_003491.4 link	n.4861G>T	non_coding_transcript_exon_variant	Exon 5 of 5
MIAT	NR_033319.3 link	n.4735G>T	non_coding_transcript_exon_variant	Exon 4 of 4
MIAT	NR_033320.3 link	n.4787G>T	non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIAT	ENST00000613780.4 link	n.4929G>T	non_coding_transcript_exon_variant	Exon 5 of 5	1
MIAT	ENST00000616213.4 link	n.4729G>T	non_coding_transcript_exon_variant	Exon 4 of 4	1
MIAT	ENST00000616469.4 link	n.4855G>T	non_coding_transcript_exon_variant	Exon 4 of 4	1

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

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

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 v4.3

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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22-26671261-G-T

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