ENST00000620145.6:n.1850G>A

Variant names:

• chr22-26668324-G-A
• rs4274
• ENST00000620145.6:n.1850G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000620145.6(MIAT):​n.1850G>A 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 0.163 in 398,450 control chromosomes in the GnomAD database, including 6,313 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 0.15 (2021 hom., cov: 32)
  • Exomes 𝑓: 0.17 (4292 hom.)
• Consequence: MIAT ENST00000620145.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.984
• Publications: 16 publications found

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:):

MIATNB (HGNC:50731): (MIAT neighbor)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000620145.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIAT	NR_033320.3	MANE Select	n.1850G>A		non_coding_transcript_exon	Exon 5 of 5
	MIAT	NR_003491.4		n.1924G>A		non_coding_transcript_exon	Exon 5 of 5
	MIAT	NR_033319.3		n.1798G>A		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIAT	ENST00000620145.6	TSL:1 MANE Select	n.1850G>A		non_coding_transcript_exon	Exon 5 of 5
	MIAT	ENST00000613780.4	TSL:1	n.1992G>A		non_coding_transcript_exon	Exon 5 of 5
	MIAT	ENST00000616213.4	TSL:1	n.1792G>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22905 AN: 151978 Hom.: 2016 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.175

GnomAD4 exome AF: 0.171 AC: 42034 AN: 246354 Hom.: 4292 Cov.: 0 AF XY: 0.169 AC XY: 21142 AN XY: 124830

African (AFR) AF: 0.114 AC: 818 AN: 7180

American (AMR) AF: 0.193 AC: 1438 AN: 7434

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 1666 AN: 9240

East Asian (EAS) AF: 0.399 AC: 9128 AN: 22894

South Asian (SAS) AF: 0.244 AC: 739 AN: 3030

European-Finnish (FIN) AF: 0.114 AC: 2382 AN: 20830

Middle Eastern (MID) AF: 0.172 AC: 223 AN: 1296

European-Non Finnish (NFE) AF: 0.144 AC: 22835 AN: 158074

Other (OTH) AF: 0.171 AC: 2805 AN: 16376

GnomAD4 genome AF: 0.151 AC: 22922 AN: 152096 Hom.: 2021 Cov.: 32 AF XY: 0.151 AC XY: 11208 AN XY: 74348

African (AFR) AF: 0.111 AC: 4592 AN: 41498

American (AMR) AF: 0.184 AC: 2815 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3468

East Asian (EAS) AF: 0.384 AC: 1978 AN: 5154

South Asian (SAS) AF: 0.254 AC: 1226 AN: 4822

European-Finnish (FIN) AF: 0.105 AC: 1107 AN: 10592

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10036 AN: 67950

Other (OTH) AF: 0.175 AC: 370 AN: 2114

Alfa AF: 0.151 Hom.: 7060

Bravo AF: 0.154

Asia WGS AF: 0.269 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.74
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs4274; hg19: chr22-27064287;