dbSNP rs3809717: MIEN1:c.-238G>T (chr17-39730733-C-A) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 1P and 8B. PP3BA1

The NM_032339.5(MIEN1):c.-238G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 526,334 control chromosomes in the GnomAD database, including 20,315 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 0.23 ( 4710 hom., cov: 32)

Exomes 𝑓: 0.28 ( 15605 hom. )

Consequence

MIEN1
NM_032339.5 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.59

Publications

10 publications found

Variant links:

Genes affected

MIEN1 (HGNC:28230): (migration and invasion enhancer 1) Involved in negative regulation of apoptotic process; positive regulation of cell migration; and positive regulation of filopodium assembly. Located in several cellular components, including centriolar satellite; cytosol; and nucleoplasm. Is intrinsic component of the cytoplasmic side of the plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

MIEN1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

PP3

Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIEN1	NM_032339.5 link	c.-238G>T		upstream_gene_variant		ENST00000394231.8	NP_115715.3
MIEN1	NM_001330206.2 link	c.-238G>T		upstream_gene_variant			NP_001317135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIEN1	ENST00000394231.8 link	c.-238G>T		upstream_gene_variant		1	NM_032339.5	ENSP00000377778.3

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34332

AN:

152034

Hom.:

4710

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0719

Gnomad AMI

AF:

0.356

Gnomad AMR

AF:

0.239

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.239

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.246

GnomAD4 exome

AF:

0.284

AC:

106278

AN:

374182

Hom.:

15605

Cov.:

AF XY:

0.281

AC XY:

55197

AN XY:

196424

show subpopulations

African (AFR)

AF:

0.0733

AC:

554

AN:

7562

American (AMR)

AF:

0.232

AC:

2275

AN:

9826

Ashkenazi Jewish (ASJ)

AF:

0.309

AC:

3639

AN:

11760

East Asian (EAS)

AF:

0.261

AC:

6213

AN:

23762

South Asian (SAS)

AF:

0.233

AC:

8115

AN:

34770

European-Finnish (FIN)

AF:

0.331

AC:

9440

AN:

28544

Middle Eastern (MID)

AF:

0.278

AC:

494

AN:

1776

European-Non Finnish (NFE)

AF:

0.297

AC:

69344

AN:

233636

Other (OTH)

AF:

0.275

AC:

6204

AN:

22546

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

3804

7609

11413

15218

19022

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.226

AC:

34340

AN:

152152

Hom.:

4710

Cov.:

AF XY:

0.228

AC XY:

16958

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0718

AC:

2983

AN:

41554

American (AMR)

AF:

0.240

AC:

3665

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

1092

AN:

3470

East Asian (EAS)

AF:

0.239

AC:

1228

AN:

5148

South Asian (SAS)

AF:

0.224

AC:

1077

AN:

4816

European-Finnish (FIN)

AF:

0.337

AC:

3567

AN:

10590

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.292

AC:

19820

AN:

67962

Other (OTH)

AF:

0.245

AC:

517

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1307

2615

3922

5230

6537

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<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:

0.242

Hom.:

1020

Bravo

AF:

0.210

Asia WGS

AF:

0.251

AC:

873

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

3.3

(source)

DANN

Benign

0.56

PhyloP100

-1.6

PromoterAI

-0.062

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.53

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.53

Position offset: 2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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