Variant 22-26671261-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000613780.4(MIAT):n.4929G>T 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 0.425 in 398,356 control chromosomes in the GnomAD database, including 37,676 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 0.39 ( 12382 hom., cov: 31)

Exomes 𝑓: 0.45 ( 25294 hom. )

Consequence

MIAT
ENST00000613780.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0130

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIAT	NR_003491.4 linkuse as main transcript	n.4861G>T	non_coding_transcript_exon_variant	5/5
MIAT	NR_033319.3 linkuse as main transcript	n.4735G>T	non_coding_transcript_exon_variant	4/4
MIAT	NR_033320.3 linkuse as main transcript	n.4787G>T	non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MIAT	ENST00000613780.4 linkuse as main transcript	n.4929G>T	non_coding_transcript_exon_variant	5/5	1
MIAT	ENST00000616213.4 linkuse as main transcript	n.4729G>T	non_coding_transcript_exon_variant	4/4	1
MIAT	ENST00000616469.4 linkuse as main transcript	n.4855G>T	non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58673

AN:

151866

Hom.:

12369

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.395

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.490

Gnomad FIN

AF:

0.488

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.461

Gnomad OTH

AF:

0.419

GnomAD4 exome

AF:

0.449

AC:

110579

AN:

246372

Hom.:

25294

Cov.:

AF XY:

0.451

AC XY:

56282

AN XY:

124848

show subpopulations

Gnomad4 AFR exome

AF:

0.221

Gnomad4 AMR exome

AF:

0.407

Gnomad4 ASJ exome

AF:

0.456

Gnomad4 EAS exome

AF:

0.415

Gnomad4 SAS exome

AF:

0.503

Gnomad4 FIN exome

AF:

0.488

Gnomad4 NFE exome

AF:

0.462

Gnomad4 OTH exome

AF:

0.426

GnomAD4 genome

AF:

0.386

AC:

58724

AN:

151984

Hom.:

12382

Cov.:

AF XY:

0.389

AC XY:

28898

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.216

Gnomad4 AMR

AF:

0.395

Gnomad4 ASJ

AF:

0.447

Gnomad4 EAS

AF:

0.384

Gnomad4 SAS

AF:

0.489

Gnomad4 FIN

AF:

0.488

Gnomad4 NFE

AF:

0.461

Gnomad4 OTH

AF:

0.425

Alfa

AF:

0.432

Hom.:

2991

Bravo

AF:

0.369

Asia WGS

AF:

0.458

AC:

1594

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.9

DANN

Benign

0.47

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over