Variant 22-26670056-A-AT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NR_003491.4(MIAT):n.3671dupT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.36 ( 9433 hom., cov: 0)

Exomes 𝑓: 0.30 ( 2 hom. )

Consequence

MIAT
NR_003491.4 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.295

Variant links:

Genes affected

MIAT (HGNC:):

MIAT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 22-26670056-A-AT is Benign according to our data. Variant chr22-26670056-A-AT is described in ClinVar as [Benign]. Clinvar id is 3055781.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIAT	NR_003491.4 linkuse as main transcript	n.3671dupT	non_coding_transcript_exon_variant	5/5
MIAT	NR_033319.3 linkuse as main transcript	n.3545dupT	non_coding_transcript_exon_variant	4/4
MIAT	NR_033320.3 linkuse as main transcript	n.3597dupT	non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MIAT	ENST00000613780.4 linkuse as main transcript	n.3739dupT	non_coding_transcript_exon_variant	5/5	1
MIAT	ENST00000616213.4 linkuse as main transcript	n.3539dupT	non_coding_transcript_exon_variant	4/4	1
MIAT	ENST00000616469.4 linkuse as main transcript	n.3665dupT	non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

51272

AN:

142008

Hom.:

9440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.531

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.433

Gnomad EAS

AF:

0.575

Gnomad SAS

AF:

0.438

Gnomad FIN

AF:

0.394

Gnomad MID

AF:

0.378

Gnomad NFE

AF:

0.359

Gnomad OTH

AF:

0.373

GnomAD4 exome

AF:

0.299

AC:

71857

AN:

240370

Hom.:

Cov.:

AF XY:

0.300

AC XY:

36533

AN XY:

121774

show subpopulations

Gnomad4 AFR exome

AF:

0.260

Gnomad4 AMR exome

AF:

0.261

Gnomad4 ASJ exome

AF:

0.316

Gnomad4 EAS exome

AF:

0.387

Gnomad4 SAS exome

AF:

0.327

Gnomad4 FIN exome

AF:

0.306

Gnomad4 NFE exome

AF:

0.287

Gnomad4 OTH exome

AF:

0.304

GnomAD4 genome

AF:

0.361

AC:

51258

AN:

142000

Hom.:

9433

Cov.:

AF XY:

0.364

AC XY:

24809

AN XY:

68152

show subpopulations

Gnomad4 AFR

AF:

0.322

Gnomad4 AMR

AF:

0.333

Gnomad4 ASJ

AF:

0.433

Gnomad4 EAS

AF:

0.575

Gnomad4 SAS

AF:

0.438

Gnomad4 FIN

AF:

0.394

Gnomad4 NFE

AF:

0.359

Gnomad4 OTH

AF:

0.371

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MIAT-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 27, 2020

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over