rs6598163

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

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

The NM_016155.7(MMP17):c.544G>A(p.Ala182Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 1,606,054 control chromosomes in the GnomAD database, including 183,664 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.46 ( 16422 hom., cov: 35)

Exomes 𝑓: 0.48 ( 167242 hom. )

Consequence

MMP17
NM_016155.7 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.539

Publications

41 publications found

Variant links:

Genes affected

MMP17 (HGNC:7163): (matrix metallopeptidase 17) This gene encodes a member of the peptidase M10 family and membrane-type subfamily of matrix metalloproteinases (MMPs). Proteins in this family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Members of this subfamily contain a transmembrane domain suggesting that these proteins are expressed at the cell surface rather than secreted. The encoded preproprotein is proteolytically processed to generate the mature protease. This protein is unique among the membrane-type matrix metalloproteinases in that it is anchored to the cell membrane via a glycosylphosphatidylinositol (GPI) anchor. Elevated expression of the encoded protein has been observed in osteoarthritis and multiple human cancers. [provided by RefSeq, Jan 2016]

MMP17 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_016155.7, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=4.464984E-4).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016155.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MMP17	NM_016155.7	MANE Select	c.544G>A	p.Ala182Thr	missense	Exon 4 of 10	NP_057239.4
MMP17	NM_001411000.1		c.292G>A	p.Ala98Thr	missense	Exon 4 of 10	NP_001397929.1	Q9ULZ9-2
MMP17	NR_182296.1		n.646G>A		non_coding_transcript_exon	Exon 4 of 11

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MMP17	ENST00000360564.5	TSL:1 MANE Select	c.544G>A	p.Ala182Thr	missense	Exon 4 of 10	ENSP00000353767.1	Q9ULZ9-1
MMP17	ENST00000535291.5	TSL:1	c.292G>A	p.Ala98Thr	missense	Exon 3 of 9	ENSP00000441106.1	Q9ULZ9-2
MMP17	ENST00000912510.1		c.562G>A	p.Ala188Thr	missense	Exon 5 of 11	ENSP00000582569.1

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70584

AN:

152078

Hom.:

16410

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.401

Gnomad AMR

AF:

0.459

Gnomad ASJ

AF:

0.472

Gnomad EAS

AF:

0.505

Gnomad SAS

AF:

0.410

Gnomad FIN

AF:

0.480

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.467

GnomAD2 exomes

AF:

0.473

AC:

115453

AN:

244164

AF XY:

0.470

show subpopulations

Gnomad AFR exome

AF:

0.424

Gnomad AMR exome

AF:

0.477

Gnomad ASJ exome

AF:

0.467

Gnomad EAS exome

AF:

0.520

Gnomad FIN exome

AF:

0.478

Gnomad NFE exome

AF:

0.489

Gnomad OTH exome

AF:

0.469

GnomAD4 exome

AF:

0.479

AC:

696056

AN:

1453856

Hom.:

167242

Cov.:

AF XY:

0.476

AC XY:

344673

AN XY:

723648

show subpopulations

African (AFR)

AF:

0.432

AC:

14464

AN:

33472

American (AMR)

AF:

0.476

AC:

21287

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.476

AC:

12427

AN:

26128

East Asian (EAS)

AF:

0.486

AC:

19280

AN:

39692

South Asian (SAS)

AF:

0.405

AC:

34926

AN:

86258

European-Finnish (FIN)

AF:

0.489

AC:

22308

AN:

45600

Middle Eastern (MID)

AF:

0.439

AC:

2530

AN:

5768

European-Non Finnish (NFE)

AF:

0.486

AC:

540765

AN:

1111882

Other (OTH)

AF:

0.465

AC:

28069

AN:

60336

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

25217

50433

75650

100866

126083

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15846

31692

47538

63384

79230

<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:

0.464

AC:

70631

AN:

152198

Hom.:

16422

Cov.:

AF XY:

0.460

AC XY:

34241

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.424

AC:

17617

AN:

41542

American (AMR)

AF:

0.459

AC:

7027

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.472

AC:

1639

AN:

3472

East Asian (EAS)

AF:

0.505

AC:

2612

AN:

5168

South Asian (SAS)

AF:

0.409

AC:

1976

AN:

4828

European-Finnish (FIN)

AF:

0.480

AC:

5091

AN:

10600

Middle Eastern (MID)

AF:

0.398

AC:

117

AN:

294

European-Non Finnish (NFE)

AF:

0.489

AC:

33206

AN:

67974

Other (OTH)

AF:

0.464

AC:

980

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

2009

4017

6026

8034

10043

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

658

1316

1974

2632

3290

<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:

0.484

Hom.:

52275

Bravo

AF:

0.462

Asia WGS

AF:

0.456

AC:

1591

AN:

3478

EpiCase

AF:

0.485

EpiControl

AF:

0.483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.063

BayesDel_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.66

CADD

Benign

0.0010

(source)

DANN

Benign

0.96

DEOGEN2

Benign

0.024

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.082

LIST_S2

Benign

0.068

MetaRNN

Benign

0.00045

MetaSVM

Benign

-0.90

MutationAssessor

Benign

-0.050

PhyloP100

-0.54

PrimateAI

Benign

0.30

PROVEAN

Benign

0.45

REVEL

Benign

0.020

Sift

Benign

0.20

Sift4G

Benign

0.52

Varity_R

0.019

gMVP

0.27

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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