Variant chr22-26666705-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.1505G>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 0.134 in 398,554 control chromosomes in the GnomAD database, including 3,795 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.14 ( 1665 hom., cov: 32)

Exomes 𝑓: 0.13 ( 2130 hom. )

Consequence

MIAT
NR_003491.3 non_coding_transcript_exon

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0440

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=-0.83).

BP6

Variant 22-26666705-G-A is Benign according to our data. Variant chr22-26666705-G-A is described in ClinVar as [Benign]. Clinvar id is 2691796.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIAT	NR_003491.3 linkuse as main transcript	n.1505G>A	non_coding_transcript_exon_variant	3/5
MIAT	NR_033319.2 linkuse as main transcript	n.1505G>A	non_coding_transcript_exon_variant	3/4
MIAT	NR_033320.2 linkuse as main transcript	n.1431G>A	non_coding_transcript_exon_variant	3/5
MIAT	NR_033321.2 linkuse as main transcript	n.1431G>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.1904G>A		non_coding_transcript_exon_variant	4/6

Frequencies

GnomAD3 genomes

AF:

0.143

AC:

21723

AN:

152076

Hom.:

1661

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.261

Gnomad AMR

AF:

0.0951

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.0820

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.125

GnomAD4 exome

AF:

0.129

AC:

31742

AN:

246360

Hom.:

2130

Cov.:

AF XY:

0.130

AC XY:

16198

AN XY:

124840

show subpopulations

Gnomad4 AFR exome

AF:

0.179

Gnomad4 AMR exome

AF:

0.0817

Gnomad4 ASJ exome

AF:

0.120

Gnomad4 EAS exome

AF:

0.0707

Gnomad4 SAS exome

AF:

0.0818

Gnomad4 FIN exome

AF:

0.157

Gnomad4 NFE exome

AF:

0.134

Gnomad4 OTH exome

AF:

0.137

GnomAD4 genome

AF:

0.143

AC:

21744

AN:

152194

Hom.:

1665

Cov.:

AF XY:

0.143

AC XY:

10650

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.184

Gnomad4 AMR

AF:

0.0948

Gnomad4 ASJ

AF:

0.132

Gnomad4 EAS

AF:

0.102

Gnomad4 SAS

AF:

0.0827

Gnomad4 FIN

AF:

0.158

Gnomad4 NFE

AF:

0.133

Gnomad4 OTH

AF:

0.124

Alfa

AF:

0.133

Hom.:

641

Bravo

AF:

0.141

Asia WGS

AF:

0.0880

AC:

305

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

Jan 28, 2020

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

-0.83

CADD

Benign

1.8

DANN

Benign

0.68

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