dbSNP rs4274: MIAT:n.1992G>A (chr22-26668324-G-A) – 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.1992G>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 0.163 in 398,450 control chromosomes in the GnomAD database, including 6,313 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 0.15 ( 2021 hom., cov: 32)

Exomes 𝑓: 0.17 ( 4292 hom. )

Consequence

MIAT
ENST00000613780.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.984

Publications

16 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:

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIAT	NR_003491.4 link	n.1924G>A	non_coding_transcript_exon_variant	Exon 5 of 5
MIAT	NR_033319.3 link	n.1798G>A	non_coding_transcript_exon_variant	Exon 4 of 4
MIAT	NR_033320.3 link	n.1850G>A	non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIAT	ENST00000613780.4 link	n.1992G>A	non_coding_transcript_exon_variant	Exon 5 of 5	1
MIAT	ENST00000616213.4 link	n.1792G>A	non_coding_transcript_exon_variant	Exon 4 of 4	1
MIAT	ENST00000616469.4 link	n.1918G>A	non_coding_transcript_exon_variant	Exon 4 of 4	1

Frequencies

GnomAD3 genomes

AF:

0.151

AC:

22905

AN:

151978

Hom.:

2016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.159

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.383

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.148

Gnomad OTH

AF:

0.175

GnomAD4 exome

AF:

0.171

AC:

42034

AN:

246354

Hom.:

4292

Cov.:

AF XY:

0.169

AC XY:

21142

AN XY:

124830

show subpopulations

African (AFR)

AF:

0.114

AC:

818

AN:

7180

American (AMR)

AF:

0.193

AC:

1438

AN:

7434

Ashkenazi Jewish (ASJ)

AF:

0.180

AC:

1666

AN:

9240

East Asian (EAS)

AF:

0.399

AC:

9128

AN:

22894

South Asian (SAS)

AF:

0.244

AC:

739

AN:

3030

European-Finnish (FIN)

AF:

0.114

AC:

2382

AN:

20830

Middle Eastern (MID)

AF:

0.172

AC:

223

AN:

1296

European-Non Finnish (NFE)

AF:

0.144

AC:

22835

AN:

158074

Other (OTH)

AF:

0.171

AC:

2805

AN:

16376

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

2298

4595

6893

9190

11488

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

164

328

492

656

820

<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:

0.151

AC:

22922

AN:

152096

Hom.:

2021

Cov.:

AF XY:

0.151

AC XY:

11208

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.111

AC:

4592

AN:

41498

American (AMR)

AF:

0.184

AC:

2815

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

614

AN:

3468

East Asian (EAS)

AF:

0.384

AC:

1978

AN:

5154

South Asian (SAS)

AF:

0.254

AC:

1226

AN:

4822

European-Finnish (FIN)

AF:

0.105

AC:

1107

AN:

10592

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.148

AC:

10036

AN:

67950

Other (OTH)

AF:

0.175

AC:

370

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

972

1945

2917

3890

4862

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

266

532

798

1064

1330

<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:

0.151

Hom.:

7060

Bravo

AF:

0.154

Asia WGS

AF:

0.269

AC:

932

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.1

(source)

DANN

Benign

0.74

PhyloP100

0.98

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