rs1018833

Variant names:

• chr22-26653047-C-T
• rs1018833
• ENST00000418918.6:n.543+6088C>T

Variant summary

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

The ENST00000418918.6(MIAT):​n.543+6088C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,908 control chromosomes in the GnomAD database, including 11,970 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 0.40 (11970 hom., cov: 31)
• Consequence: MIAT ENST00000418918.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• 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)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418918.6. 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_185982.1		n.531+6088C>T		intron	N/A
	MIAT	NR_185983.1		n.531+6088C>T		intron	N/A
	MIAT	NR_185984.1		n.531+6088C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIAT	ENST00000418918.6	TSL:4	n.543+6088C>T		intron	N/A
	MIAT	ENST00000421867.6	TSL:4	n.539+6088C>T		intron	N/A
	MIAT	ENST00000430483.5	TSL:4	n.113+5707C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60143 AN: 151790 Hom.: 11957 Cov.: 31

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.396 AC: 60208 AN: 151908 Hom.: 11970 Cov.: 31 AF XY: 0.397 AC XY: 29473 AN XY: 74230

African (AFR) AF: 0.429 AC: 17782 AN: 41422

American (AMR) AF: 0.358 AC: 5465 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1411 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1693 AN: 5146

South Asian (SAS) AF: 0.418 AC: 2012 AN: 4814

European-Finnish (FIN) AF: 0.430 AC: 4522 AN: 10510

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26058 AN: 67960

Other (OTH) AF: 0.414 AC: 874 AN: 2112

Alfa AF: 0.392 Hom.: 8137

Bravo AF: 0.393

Asia WGS AF: 0.414 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.2
DANN	Benign	0.81
PhyloP100		-0.60

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: rs1018833;

hg19: chr22-27049011;