Variant chr22-26670771-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NR_003491.3(MIAT):n.4477T>C 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 0.00771 in 398,556 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0069 ( 10 hom., cov: 31)

Exomes 𝑓: 0.0082 ( 12 hom. )

Consequence

MIAT
NR_003491.3 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.105

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:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 22-26670771-T-C is Benign according to our data. Variant chr22-26670771-T-C is described in ClinVar as [Benign]. Clinvar id is 2653010.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0082 (2020/246306) while in subpopulation MID AF= 0.0263 (34/1294). AF 95% confidence interval is 0.0193. There are 12 homozygotes in gnomad4_exome. There are 990 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 10 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIAT	NR_003491.3 linkuse as main transcript	n.4477T>C	non_coding_transcript_exon_variant	5/5
MIAT	NR_033319.2 linkuse as main transcript	n.4351T>C	non_coding_transcript_exon_variant	4/4
MIAT	NR_033320.2 linkuse as main transcript	n.4403T>C	non_coding_transcript_exon_variant	5/5
MIAT	NR_033321.2 linkuse as main transcript	n.4277T>C	non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000382641.1 linkuse as main transcript	n.977+907A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00692

AC:

1052

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0112

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.0140

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00879

Gnomad OTH

AF:

0.00862

GnomAD4 exome

AF:

0.00820

AC:

2020

AN:

246306

Hom.:

Cov.:

AF XY:

0.00793

AC XY:

990

AN XY:

124800

show subpopulations

Gnomad4 AFR exome

AF:

0.00139

Gnomad4 AMR exome

AF:

0.00511

Gnomad4 ASJ exome

AF:

0.0150

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00297

Gnomad4 FIN exome

AF:

0.0108

Gnomad4 NFE exome

AF:

0.00903

Gnomad4 OTH exome

AF:

0.00849

GnomAD4 genome

AF:

0.00691

AC:

1052

AN:

152250

Hom.:

Cov.:

AF XY:

0.00725

AC XY:

540

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.00120

Gnomad4 AMR

AF:

0.0112

Gnomad4 ASJ

AF:

0.0130

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00270

Gnomad4 FIN

AF:

0.0140

Gnomad4 NFE

AF:

0.00879

Gnomad4 OTH

AF:

0.00853

Alfa

AF:

0.00773

Hom.:

Bravo

AF:

0.00631

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2023

MIAT: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.7

DANN

Benign

0.58

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