rs763271
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000643270.1(MIAT):n.604C>G 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 0.277 in 397,784 control chromosomes in the GnomAD database, including 16,113 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.26 ( 5360 hom., cov: 29)
Exomes 𝑓: 0.29 ( 10753 hom. )
Consequence
MIAT
ENST00000643270.1 non_coding_transcript_exon
ENST00000643270.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.131
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIAT | ENST00000643270.1 | n.604C>G | non_coding_transcript_exon_variant | 2/6 |
Frequencies
GnomAD3 genomes ? AF: 0.262 AC: 39674AN: 151406Hom.: 5360 Cov.: 29
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GnomAD4 exome AF: 0.286 AC: 70501AN: 246258Hom.: 10753 Cov.: 0 AF XY: 0.285 AC XY: 35604AN XY: 124778
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GnomAD4 genome ? AF: 0.262 AC: 39688AN: 151526Hom.: 5360 Cov.: 29 AF XY: 0.264 AC XY: 19537AN XY: 74022
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at