dbSNP rs4553158: MIER1:c.773-45A>G (chr1-66970763-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001077700.3(MIER1):c.773-45A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,393,584 control chromosomes in the GnomAD database, including 18,907 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 0.12 ( 1471 hom., cov: 32)

Exomes 𝑓: 0.16 ( 17436 hom. )

Consequence

MIER1
NM_001077700.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.62

Publications

5 publications found

Variant links:

Genes affected

MIER1 (HGNC:29657): (MIER1 transcriptional regulator) This gene encodes a protein that was first identified in Xenopus laevis by its role in a mesoderm induction early response (MIER). The encoded protein functions as a transcriptional regulator. Alternatively spliced transcript variants encode multiple isoforms, some of which lack a C-terminal nuclear localization signal. [provided by RefSeq, May 2013]

MIER1 links:

Genome browser will be placed here

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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIER1	NM_001077700.3 link	c.773-45A>G		intron_variant	Intron 8 of 13	ENST00000401041.6	NP_001071168.2	Q8N108-12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIER1	ENST00000401041.6 link	c.773-45A>G		intron_variant	Intron 8 of 13	2	NM_001077700.3	ENSP00000383820.1		Q8N108-12

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18481

AN:

152048

Hom.:

1474

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0338

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.0960

Gnomad ASJ

AF:

0.106

Gnomad EAS

AF:

0.0802

Gnomad SAS

AF:

0.0918

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.169

Gnomad OTH

AF:

0.132

GnomAD2 exomes

AF:

0.144

AC:

22602

AN:

157038

AF XY:

0.147

show subpopulations

Gnomad AFR exome

AF:

0.0309

Gnomad AMR exome

AF:

0.0648

Gnomad ASJ exome

AF:

0.101

Gnomad EAS exome

AF:

0.0878

Gnomad FIN exome

AF:

0.239

Gnomad NFE exome

AF:

0.173

Gnomad OTH exome

AF:

0.166

GnomAD4 exome

AF:

0.162

AC:

201495

AN:

1241418

Hom.:

17436

Cov.:

AF XY:

0.161

AC XY:

98901

AN XY:

615156

show subpopulations

African (AFR)

AF:

0.0267

AC:

696

AN:

26110

American (AMR)

AF:

0.0740

AC:

1751

AN:

23668

Ashkenazi Jewish (ASJ)

AF:

0.111

AC:

2168

AN:

19538

East Asian (EAS)

AF:

0.0640

AC:

2252

AN:

35164

South Asian (SAS)

AF:

0.0921

AC:

5589

AN:

60716

European-Finnish (FIN)

AF:

0.241

AC:

12029

AN:

49882

Middle Eastern (MID)

AF:

0.0945

AC:

473

AN:

5006

European-Non Finnish (NFE)

AF:

0.174

AC:

168568

AN:

969414

Other (OTH)

AF:

0.153

AC:

7969

AN:

51920

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

7818

15636

23455

31273

39091

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5852

11704

17556

23408

29260

<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:

0.121

AC:

18474

AN:

152166

Hom.:

1471

Cov.:

AF XY:

0.122

AC XY:

9094

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.0337

AC:

1400

AN:

41568

American (AMR)

AF:

0.0958

AC:

1465

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.106

AC:

369

AN:

3470

East Asian (EAS)

AF:

0.0794

AC:

412

AN:

5190

South Asian (SAS)

AF:

0.0923

AC:

446

AN:

4830

European-Finnish (FIN)

AF:

0.236

AC:

2493

AN:

10582

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.169

AC:

11465

AN:

67918

Other (OTH)

AF:

0.133

AC:

281

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

815

1631

2446

3262

4077

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.148

Hom.:

5567

Bravo

AF:

0.107

Asia WGS

AF:

0.0960

AC:

335

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.11

(source)

DANN

Benign

0.34

PhyloP100

-2.6

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over