rs739310

chr22-26655335-A-Gchr22-26655335-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000643270.1(MIAT):n.647-7981A>G 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 0.178 in 152,236 control chromosomes in the GnomAD database, including 2,733 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 0.18 (2733 hom., cov: 33)
• Consequence: MIAT ENST00000643270.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 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.647-7981A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27026 AN: 152118 Hom.: 2729 Cov.: 33

Gnomad AFR AF: 0.0995

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.202

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.178 AC: 27039 AN: 152236 Hom.: 2733 Cov.: 33 AF XY: 0.176 AC XY: 13132 AN XY: 74422

Gnomad4 AFR AF: 0.0997

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.200

Alfa AF: 0.200 Hom.: 6631

Bravo AF: 0.181

Asia WGS AF: 0.256 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.6
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs739310; hg19: chr22-27051299;