Variant chr22-26666628-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NR_003491.3(MIAT):n.1428G>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 0.0797 in 398,646 control chromosomes in the GnomAD database, including 1,449 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.069 ( 435 hom., cov: 32)

Exomes 𝑓: 0.086 ( 1014 hom. )

Consequence

MIAT
NR_003491.3 non_coding_transcript_exon

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.621

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 22-26666628-G-A is Benign according to our data. Variant chr22-26666628-G-A is described in ClinVar as [Benign]. Clinvar id is 3057049.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIAT	NR_003491.3 linkuse as main transcript	n.1428G>A	non_coding_transcript_exon_variant	3/5
MIAT	NR_033319.2 linkuse as main transcript	n.1428G>A	non_coding_transcript_exon_variant	3/4
MIAT	NR_033320.2 linkuse as main transcript	n.1354G>A	non_coding_transcript_exon_variant	3/5
MIAT	NR_033321.2 linkuse as main transcript	n.1354G>A	non_coding_transcript_exon_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIAT	ENST00000643270.1 linkuse as main transcript	n.1827G>A		non_coding_transcript_exon_variant	4/6

Frequencies

GnomAD3 genomes

AF:

0.0689

AC:

10490

AN:

152162

Hom.:

436

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0158

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.0725

Gnomad ASJ

AF:

0.121

Gnomad EAS

AF:

0.0716

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0861

Gnomad OTH

AF:

0.0707

GnomAD4 exome

AF:

0.0864

AC:

21276

AN:

246366

Hom.:

1014

Cov.:

AF XY:

0.0867

AC XY:

10821

AN XY:

124840

show subpopulations

Gnomad4 AFR exome

AF:

0.0175

Gnomad4 AMR exome

AF:

0.0644

Gnomad4 ASJ exome

AF:

0.110

Gnomad4 EAS exome

AF:

0.0635

Gnomad4 SAS exome

AF:

0.108

Gnomad4 FIN exome

AF:

0.119

Gnomad4 NFE exome

AF:

0.0879

Gnomad4 OTH exome

AF:

0.0834

GnomAD4 genome

AF:

0.0688

AC:

10481

AN:

152280

Hom.:

435

Cov.:

AF XY:

0.0702

AC XY:

5223

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0157

Gnomad4 AMR

AF:

0.0723

Gnomad4 ASJ

AF:

0.121

Gnomad4 EAS

AF:

0.0715

Gnomad4 SAS

AF:

0.103

Gnomad4 FIN

AF:

0.123

Gnomad4 NFE

AF:

0.0861

Gnomad4 OTH

AF:

0.0690

Alfa

AF:

0.0732

Hom.:

Bravo

AF:

0.0628

Asia WGS

AF:

0.100

AC:

348

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MIAT-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 24, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.96

DANN

Benign

0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over