chr22-26670601-T-TTAAA

Position:

• chr22-26670601-T-TTAAA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The ENST00000613780.4(MIAT):​n.4270_4273dupTAAA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 11)
• Consequence: MIAT ENST00000613780.4 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.176

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]

ENSG00000206028 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 22-26670601-T-TTAAA is Benign according to our data. Variant chr22-26670601-T-TTAAA is described in ClinVar as [Likely_benign]. Clinvar id is 3036351.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIAT	NR_003491.4	n.4202_4205dupTAAA		non_coding_transcript_exon_variant	5/5
MIAT	NR_033319.3	n.4076_4079dupTAAA		non_coding_transcript_exon_variant	4/4
MIAT	NR_033320.3	n.4128_4131dupTAAA		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIAT	ENST00000613780.4	n.4270_4273dupTAAA		non_coding_transcript_exon_variant	5/5	1
MIAT	ENST00000616213.4	n.4070_4073dupTAAA		non_coding_transcript_exon_variant	4/4	1
MIAT	ENST00000616469.4	n.4196_4199dupTAAA		non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes Cov.: 11

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 11

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

MIAT-related disorder Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 21, 2023

This variant is classified as likely 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

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-27066564;