Variant rs252890 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000381199.8(MIER3):c.829+81A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 1,134,892 control chromosomes in the GnomAD database, including 200,211 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 0.50 ( 21457 hom., cov: 31)

Exomes 𝑓: 0.59 ( 178754 hom. )

Consequence

MIER3
ENST00000381199.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.519

Variant links:

Genes affected

MIER3 (HGNC:26678): (MIER family member 3) Predicted to enable histone deacetylase binding activity and transcription corepressor activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

MIER3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIER3	NM_001297599.2 linkuse as main transcript	c.829+81A>G		intron_variant		ENST00000381199.8	NP_001284528.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIER3	ENST00000381199.8 linkuse as main transcript	c.829+81A>G		intron_variant		1	NM_001297599.2	ENSP00000370596	A1	Q7Z3K6-1

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76529

AN:

151830

Hom.:

21455

Cov.:

show subpopulations

Gnomad AFR

AF:

0.304

Gnomad AMI

AF:

0.593

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.660

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.649

Gnomad MID

AF:

0.571

Gnomad NFE

AF:

0.645

Gnomad OTH

AF:

0.536

GnomAD4 exome

AF:

0.588

AC:

577515

AN:

982942

Hom.:

178754

AF XY:

0.584

AC XY:

297930

AN XY:

509856

show subpopulations

Gnomad4 AFR exome

AF:

0.305

Gnomad4 AMR exome

AF:

0.348

Gnomad4 ASJ exome

AF:

0.667

Gnomad4 EAS exome

AF:

0.115

Gnomad4 SAS exome

AF:

0.448

Gnomad4 FIN exome

AF:

0.650

Gnomad4 NFE exome

AF:

0.648

Gnomad4 OTH exome

AF:

0.567

GnomAD4 genome

AF:

0.504

AC:

76560

AN:

151950

Hom.:

21457

Cov.:

AF XY:

0.498

AC XY:

36966

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.305

Gnomad4 AMR

AF:

0.430

Gnomad4 ASJ

AF:

0.660

Gnomad4 EAS

AF:

0.110

Gnomad4 SAS

AF:

0.425

Gnomad4 FIN

AF:

0.649

Gnomad4 NFE

AF:

0.645

Gnomad4 OTH

AF:

0.532

Alfa

AF:

0.605

Hom.:

16124

Bravo

AF:

0.478

Asia WGS

AF:

0.298

AC:

1036

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

6.5

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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