22-26662857-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_003491.3(MIAT):​n.174-459C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,068 control chromosomes in the GnomAD database, including 1,053 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 0.11 ( 1053 hom., cov: 32)

Consequence

MIAT
NR_003491.3 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.228
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]

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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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MIATNR_003491.3 linkuse as main transcriptn.174-459C>T intron_variant, non_coding_transcript_variant
MIATNR_033319.2 linkuse as main transcriptn.174-459C>T intron_variant, non_coding_transcript_variant
MIATNR_033320.2 linkuse as main transcriptn.174-459C>T intron_variant, non_coding_transcript_variant
MIATNR_033321.2 linkuse as main transcriptn.174-459C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MIATENST00000643270.1 linkuse as main transcriptn.647-459C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.109
AC:
16490
AN:
151950
Hom.:
1051
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0488
Gnomad AMI
AF:
0.262
Gnomad AMR
AF:
0.0853
Gnomad ASJ
AF:
0.129
Gnomad EAS
AF:
0.105
Gnomad SAS
AF:
0.0823
Gnomad FIN
AF:
0.180
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.138
Gnomad OTH
AF:
0.100
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.108
AC:
16496
AN:
152068
Hom.:
1053
Cov.:
32
AF XY:
0.111
AC XY:
8247
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.0487
Gnomad4 AMR
AF:
0.0851
Gnomad4 ASJ
AF:
0.129
Gnomad4 EAS
AF:
0.105
Gnomad4 SAS
AF:
0.0832
Gnomad4 FIN
AF:
0.180
Gnomad4 NFE
AF:
0.138
Gnomad4 OTH
AF:
0.0992
Alfa
AF:
0.127
Hom.:
1170
Bravo
AF:
0.0992
Asia WGS
AF:
0.0860
AC:
299
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
4.0
DANN
Benign
0.92

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.

Other links and lift over

dbSNP: rs2331291; hg19: chr22-27058821; API