rs763271

Variant names:

• chr22-26647269-C-G
• rs763271
• ENST00000430483.5:n.42C>G

Variant summary

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

The ENST00000430483.5(MIAT):​n.42C>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 ENST00000430483.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 4 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]

MIATNB (HGNC:50731): (MIAT neighbor)

ENSG00000309298 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430483.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIAT	NR_185987.1		n.627C>G		non_coding_transcript_exon	Exon 2 of 5
	MIAT	NR_185982.1		n.531+310C>G		intron	N/A
	MIAT	NR_185983.1		n.531+310C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIAT	ENST00000430483.5	TSL:4	n.42C>G		non_coding_transcript_exon	Exon 1 of 4
	MIAT	ENST00000440347.5	TSL:4	n.59C>G		non_coding_transcript_exon	Exon 1 of 4
	MIAT	ENST00000450203.6	TSL:4	n.46C>G		non_coding_transcript_exon	Exon 1 of 5

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39674 AN: 151406 Hom.: 5360 Cov.: 29

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.277

GnomAD4 exome AF: 0.286 AC: 70501 AN: 246258 Hom.: 10753 Cov.: 0 AF XY: 0.285 AC XY: 35604 AN XY: 124778

African (AFR) AF: 0.211 AC: 1511 AN: 7178

American (AMR) AF: 0.256 AC: 1901 AN: 7434

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 3171 AN: 9238

East Asian (EAS) AF: 0.459 AC: 10503 AN: 22892

South Asian (SAS) AF: 0.369 AC: 1117 AN: 3028

European-Finnish (FIN) AF: 0.283 AC: 5893 AN: 20812

Middle Eastern (MID) AF: 0.287 AC: 372 AN: 1294

European-Non Finnish (NFE) AF: 0.262 AC: 41417 AN: 158016

Other (OTH) AF: 0.282 AC: 4616 AN: 16366

GnomAD4 genome AF: 0.262 AC: 39688 AN: 151526 Hom.: 5360 Cov.: 29 AF XY: 0.264 AC XY: 19537 AN XY: 74022

African (AFR) AF: 0.208 AC: 8598 AN: 41242

American (AMR) AF: 0.262 AC: 3991 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1210 AN: 3472

East Asian (EAS) AF: 0.435 AC: 2230 AN: 5122

South Asian (SAS) AF: 0.373 AC: 1782 AN: 4778

European-Finnish (FIN) AF: 0.285 AC: 2981 AN: 10470

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17968 AN: 67898

Other (OTH) AF: 0.274 AC: 578 AN: 2106

Alfa AF: 0.254 Hom.: 603

Bravo AF: 0.257

Asia WGS AF: 0.365 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.49
PhyloP100		-0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs763271;

hg19: chr22-27043233;