Variant rs832529 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001297599.2(MIER3):c.596-63G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 1,428,914 control chromosomes in the GnomAD database, including 265,900 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 ( 21466 hom., cov: 33)

Exomes 𝑓: 0.61 ( 244434 hom. )

Consequence

MIER3
NM_001297599.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.563

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=-0.8).

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.596-63G>A		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.596-63G>A		intron_variant		1	NM_001297599.2	ENSP00000370596	A1	Q7Z3K6-1

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76549

AN:

152030

Hom.:

21464

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.593

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.660

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.649

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.645

Gnomad OTH

AF:

0.536

GnomAD4 exome

AF:

0.608

AC:

775881

AN:

1276766

Hom.:

244434

AF XY:

0.605

AC XY:

382119

AN XY:

632000

show subpopulations

Gnomad4 AFR exome

AF:

0.296

Gnomad4 AMR exome

AF:

0.346

Gnomad4 ASJ exome

AF:

0.666

Gnomad4 EAS exome

AF:

0.117

Gnomad4 SAS exome

AF:

0.447

Gnomad4 FIN exome

AF:

0.650

Gnomad4 NFE exome

AF:

0.649

Gnomad4 OTH exome

AF:

0.573

GnomAD4 genome

AF:

0.503

AC:

76579

AN:

152148

Hom.:

21466

Cov.:

AF XY:

0.497

AC XY:

36978

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.431

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:

0.582

Hom.:

12274

Bravo

AF:

0.477

Asia WGS

AF:

0.298

AC:

1037

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.5

DANN

Benign

0.64

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