Genetic Variant MIER3:c.829+81A>G (chr5-56930583-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001297598.2(MIER3):c.844+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
NM_001297598.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.519

Publications

16 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001297598.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MIER3	NM_001297599.2	MANE Select	c.829+81A>G	intron	N/A	NP_001284528.1
MIER3	NM_001297598.2		c.844+81A>G	intron	N/A	NP_001284527.1
MIER3	NM_152622.5		c.829+81A>G	intron	N/A	NP_689835.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MIER3	ENST00000381199.8	TSL:1 MANE Select	c.829+81A>G	intron	N/A	ENSP00000370596.3
MIER3	ENST00000381226.7	TSL:1	c.844+81A>G	intron	N/A	ENSP00000370624.3
MIER3	ENST00000381213.7	TSL:1	c.829+81A>G	intron	N/A	ENSP00000370611.3

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

African (AFR)

AF:

0.305

AC:

7242

AN:

23780

American (AMR)

AF:

0.348

AC:

14964

AN:

43020

Ashkenazi Jewish (ASJ)

AF:

0.667

AC:

15069

AN:

22608

East Asian (EAS)

AF:

0.115

AC:

4298

AN:

37314

South Asian (SAS)

AF:

0.448

AC:

34058

AN:

75982

European-Finnish (FIN)

AF:

0.650

AC:

33808

AN:

51982

Middle Eastern (MID)

AF:

0.618

AC:

2971

AN:

4804

European-Non Finnish (NFE)

AF:

0.648

AC:

439949

AN:

679104

Other (OTH)

AF:

0.567

AC:

25156

AN:

44348

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

10883

21765

32648

43530

54413

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8584

17168

25752

34336

42920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.504

AC:

76560

AN:

151950

Hom.:

21457

Cov.:

AF XY:

0.498

AC XY:

36966

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.305

AC:

12620

AN:

41440

American (AMR)

AF:

0.430

AC:

6568

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.660

AC:

2288

AN:

3468

East Asian (EAS)

AF:

0.110

AC:

566

AN:

5168

South Asian (SAS)

AF:

0.425

AC:

2047

AN:

4812

European-Finnish (FIN)

AF:

0.649

AC:

6858

AN:

10572

Middle Eastern (MID)

AF:

0.572

AC:

167

AN:

292

European-Non Finnish (NFE)

AF:

0.645

AC:

43780

AN:

67908

Other (OTH)

AF:

0.532

AC:

1126

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1728

3457

5185

6914

8642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

660

1320

1980

2640

3300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.610

Hom.:

23669

Bravo

AF:

0.478

Asia WGS

AF:

0.298

AC:

1036

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

6.5

(source)

DANN

Benign

0.79

PhyloP100

0.52

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over