22-26670056-A-AT

Position:

• chr22-26670056-A-AT

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NR_003491.3(MIAT):​n.3777dup variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.36 (9433 hom., cov: 0)
  • Exomes 𝑓: 0.30 (2 hom.)
• Consequence: MIAT NR_003491.3 non_coding_transcript_exon
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.295

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 22-26670056-A-AT is Benign according to our data. Variant chr22-26670056-A-AT is described in ClinVar as [Benign]. Clinvar id is 3055781.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIAT	NR_003491.3	n.3777dup		non_coding_transcript_exon_variant	5/5
MIAT	NR_033319.2	n.3651dup		non_coding_transcript_exon_variant	4/4
MIAT	NR_033320.2	n.3703dup		non_coding_transcript_exon_variant	5/5
MIAT	NR_033321.2	n.3577dup		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000382641.1	n.978-619_978-618insA		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 51272 AN: 142008 Hom.: 9440 Cov.: 0

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.373

GnomAD4 exome AF: 0.299 AC: 71857 AN: 240370 Hom.: 2 Cov.: 0 AF XY: 0.300 AC XY: 36533 AN XY: 121774

Gnomad4 AFR exome AF: 0.260

Gnomad4 AMR exome AF: 0.261

Gnomad4 ASJ exome AF: 0.316

Gnomad4 EAS exome AF: 0.387

Gnomad4 SAS exome AF: 0.327

Gnomad4 FIN exome AF: 0.306

Gnomad4 NFE exome AF: 0.287

Gnomad4 OTH exome AF: 0.304

GnomAD4 genome AF: 0.361 AC: 51258 AN: 142000 Hom.: 9433 Cov.: 0 AF XY: 0.364 AC XY: 24809 AN XY: 68152

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.371

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

MIAT-related disorder Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 27, 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35523695; hg19: chr22-27066019;