rs35955962

Variant names:

• chr22-26669261-G-A
• rs35955962
• ENST00000620145.6:n.2787G>A

Variant summary

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

The ENST00000613780.4(MIAT):​n.2929G>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 0.117 in 398,564 control chromosomes in the GnomAD database, including 2,944 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as no classification for the single variant (no stars).

• Frequency:
  • Genomes: 𝑓 0.11 (971 hom., cov: 33)
  • Exomes 𝑓: 0.12 (1973 hom.)
• Consequence: MIAT ENST00000613780.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 7 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000613780.4. 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_033320.3	MANE Select	n.2787G>A		non_coding_transcript_exon	Exon 5 of 5
	MIAT	NR_003491.4		n.2861G>A		non_coding_transcript_exon	Exon 5 of 5
	MIAT	NR_033319.3		n.2735G>A		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIAT	ENST00000620145.6	TSL:1 MANE Select	n.2787G>A		non_coding_transcript_exon	Exon 5 of 5
	MIAT	ENST00000613780.4	TSL:1	n.2929G>A		non_coding_transcript_exon	Exon 5 of 5
	MIAT	ENST00000616213.4	TSL:1	n.2729G>A		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16064 AN: 152102 Hom.: 969 Cov.: 33

Gnomad AFR AF: 0.0543

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.0974

GnomAD4 exome AF: 0.124 AC: 30449 AN: 246344 Hom.: 1973 Cov.: 0 AF XY: 0.125 AC XY: 15611 AN XY: 124826

African (AFR) AF: 0.0553 AC: 397 AN: 7182

American (AMR) AF: 0.0705 AC: 524 AN: 7434

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 1079 AN: 9240

East Asian (EAS) AF: 0.0709 AC: 1624 AN: 22894

South Asian (SAS) AF: 0.0841 AC: 255 AN: 3032

European-Finnish (FIN) AF: 0.157 AC: 3261 AN: 20824

Middle Eastern (MID) AF: 0.128 AC: 166 AN: 1296

European-Non Finnish (NFE) AF: 0.134 AC: 21115 AN: 158072

Other (OTH) AF: 0.124 AC: 2028 AN: 16370

GnomAD4 genome AF: 0.106 AC: 16069 AN: 152220 Hom.: 971 Cov.: 33 AF XY: 0.107 AC XY: 7953 AN XY: 74428

African (AFR) AF: 0.0541 AC: 2249 AN: 41542

American (AMR) AF: 0.0842 AC: 1289 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3466

East Asian (EAS) AF: 0.102 AC: 530 AN: 5186

South Asian (SAS) AF: 0.0834 AC: 402 AN: 4822

European-Finnish (FIN) AF: 0.157 AC: 1657 AN: 10568

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

European-Non Finnish (NFE) AF: 0.133 AC: 9015 AN: 68012

Other (OTH) AF: 0.0964 AC: 204 AN: 2116

Alfa AF: 0.109 Hom.: 135

Bravo AF: 0.0984

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.71
PhyloP100		-0.23
Mutation Taster		=99/1	polymorphism

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: rs35955962;

hg19: chr22-27065224;