dbSNP rs763271: MIAT:n.42C>G (chr22-26647269-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000430483.5(MIAT):n.42C>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 0.277 in 397,784 control chromosomes in the GnomAD database, including 16,113 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 0.26 ( 5360 hom., cov: 29)

Exomes 𝑓: 0.29 ( 10753 hom. )

Consequence

MIAT
ENST00000430483.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.131

Publications

4 publications found

Variant links:

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:

MIATNB (HGNC:50731): (MIAT neighbor)

MIATNB links:

ENSG00000309298 (HGNC:):

ENSG00000309298 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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIAT	NR_185987.1 link	n.627C>G	non_coding_transcript_exon_variant	Exon 2 of 5
MIAT	NR_185982.1 link	n.531+310C>G	intron_variant	Intron 1 of 3
MIAT	NR_185983.1 link	n.531+310C>G	intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIAT	ENST00000430483.5 link	n.42C>G	non_coding_transcript_exon_variant	Exon 1 of 4	4
MIAT	ENST00000440347.5 link	n.59C>G	non_coding_transcript_exon_variant	Exon 1 of 4	4
MIAT	ENST00000450203.6 link	n.46C>G	non_coding_transcript_exon_variant	Exon 1 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39674

AN:

151406

Hom.:

5360

Cov.:

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.373

Gnomad FIN

AF:

0.285

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.277

GnomAD4 exome

AF:

0.286

AC:

70501

AN:

246258

Hom.:

10753

Cov.:

AF XY:

0.285

AC XY:

35604

AN XY:

124778

show subpopulations

African (AFR)

AF:

0.211

AC:

1511

AN:

7178

American (AMR)

AF:

0.256

AC:

1901

AN:

7434

Ashkenazi Jewish (ASJ)

AF:

0.343

AC:

3171

AN:

9238

East Asian (EAS)

AF:

0.459

AC:

10503

AN:

22892

South Asian (SAS)

AF:

0.369

AC:

1117

AN:

3028

European-Finnish (FIN)

AF:

0.283

AC:

5893

AN:

20812

Middle Eastern (MID)

AF:

0.287

AC:

372

AN:

1294

European-Non Finnish (NFE)

AF:

0.262

AC:

41417

AN:

158016

Other (OTH)

AF:

0.282

AC:

4616

AN:

16366

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

2618

5237

7855

10474

13092

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

242

484

726

968

1210

<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:

0.262

AC:

39688

AN:

151526

Hom.:

5360

Cov.:

AF XY:

0.264

AC XY:

19537

AN XY:

74022

show subpopulations

African (AFR)

AF:

0.208

AC:

8598

AN:

41242

American (AMR)

AF:

0.262

AC:

3991

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.349

AC:

1210

AN:

3472

East Asian (EAS)

AF:

0.435

AC:

2230

AN:

5122

South Asian (SAS)

AF:

0.373

AC:

1782

AN:

4778

European-Finnish (FIN)

AF:

0.285

AC:

2981

AN:

10470

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.265

AC:

17968

AN:

67898

Other (OTH)

AF:

0.274

AC:

578

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1429

2858

4286

5715

7144

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

428

856

1284

1712

2140

<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:

0.254

Hom.:

603

Bravo

AF:

0.257

Asia WGS

AF:

0.365

AC:

1271

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

2.2

(source)

DANN

Benign

0.49

PhyloP100

-0.13

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over