rs739310

Variant names:

• chr22-26655335-A-G
• rs739310
• ENST00000418918.6:n.544-7981A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-26655335-A-G
• chr22-26655335-A-T

Variant summary

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

The ENST00000418918.6(MIAT):​n.544-7981A>G variant causes a intron 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 ENST00000418918.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 9 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=-0.82).
• 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 rank	MANE	Protein	UniProt
MIAT	NR_185982.1	n.532-7981A>G		intron_variant	Intron 1 of 3
MIAT	NR_185983.1	n.532-7981A>G		intron_variant	Intron 1 of 4
MIAT	NR_185984.1	n.532-7981A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIAT	ENST00000418918.6	n.544-7981A>G		intron_variant	Intron 1 of 2	4
MIAT	ENST00000421867.6	n.540-7981A>G		intron_variant	Intron 1 of 2	4
MIAT	ENST00000430483.5	n.114-5364A>G		intron_variant	Intron 1 of 3	4

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

African (AFR) AF: 0.0997 AC: 4141 AN: 41548

American (AMR) AF: 0.224 AC: 3430 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3470

East Asian (EAS) AF: 0.360 AC: 1866 AN: 5180

South Asian (SAS) AF: 0.258 AC: 1244 AN: 4826

European-Finnish (FIN) AF: 0.125 AC: 1322 AN: 10602

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13636 AN: 68006

Other (OTH) AF: 0.200 AC: 423 AN: 2114

Alfa AF: 0.198 Hom.: 14198

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
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs739310; hg19: chr22-27051299;