Variant chr22-26666332-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.1132G>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 0.116 in 398,502 control chromosomes in the GnomAD database, including 2,918 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.11 ( 960 hom., cov: 32)

Exomes 𝑓: 0.12 ( 1958 hom. )

Consequence

MIAT
NR_003491.3 non_coding_transcript_exon

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.716

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=-0.9).

BP6

Variant 22-26666332-G-A is Benign according to our data. Variant chr22-26666332-G-A is described in ClinVar as [Benign]. Clinvar id is 2691795.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIAT	NR_003491.3 linkuse as main transcript	n.1132G>A	non_coding_transcript_exon_variant	3/5
MIAT	NR_033319.2 linkuse as main transcript	n.1132G>A	non_coding_transcript_exon_variant	3/4
MIAT	NR_033320.2 linkuse as main transcript	n.1058G>A	non_coding_transcript_exon_variant	3/5
MIAT	NR_033321.2 linkuse as main transcript	n.1058G>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.1531G>A		non_coding_transcript_exon_variant	4/6

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

16016

AN:

152036

Hom.:

958

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0543

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.0859

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.0790

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.0977

GnomAD4 exome

AF:

0.123

AC:

30239

AN:

246348

Hom.:

1958

Cov.:

AF XY:

0.124

AC XY:

15520

AN XY:

124830

show subpopulations

Gnomad4 AFR exome

AF:

0.0557

Gnomad4 AMR exome

AF:

0.0720

Gnomad4 ASJ exome

AF:

0.117

Gnomad4 EAS exome

AF:

0.0669

Gnomad4 SAS exome

AF:

0.0782

Gnomad4 FIN exome

AF:

0.155

Gnomad4 NFE exome

AF:

0.133

Gnomad4 OTH exome

AF:

0.124

GnomAD4 genome

AF:

0.105

AC:

16021

AN:

152154

Hom.:

960

Cov.:

AF XY:

0.107

AC XY:

7928

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0541

Gnomad4 AMR

AF:

0.0857

Gnomad4 ASJ

AF:

0.129

Gnomad4 EAS

AF:

0.101

Gnomad4 SAS

AF:

0.0799

Gnomad4 FIN

AF:

0.155

Gnomad4 NFE

AF:

0.132

Gnomad4 OTH

AF:

0.0967

Alfa

AF:

0.119

Hom.:

170

Bravo

AF:

0.0987

Asia WGS

AF:

0.0790

AC:

275

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

Aug 14, 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

-0.90

CADD

Benign

0.42

DANN

Benign

0.52

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