dbSNP rs3739382: MMP16:c.1084-74C>T (chr8-88074817-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_005941.5(MMP16):c.1084-74C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0552 in 1,506,114 control chromosomes in the GnomAD database, including 3,066 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 0.049 ( 292 hom., cov: 32)

Exomes 𝑓: 0.056 ( 2774 hom. )

Consequence

MMP16
NM_005941.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.676

Publications

4 publications found

Variant links:

Genes affected

MMP16 (HGNC:7162): (matrix metallopeptidase 16) Proteins of the matrix metalloproteinase (MMP) 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. Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. The encoded protein activates MMP2 by cleavage. This gene was once referred to as MT-MMP2, but was renamed as MT-MMP3 or MMP16. [provided by RefSeq, Oct 2010]

MMP16 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMP16	NM_005941.5 link	c.1084-74C>T		intron_variant	Intron 6 of 9	ENST00000286614.11	NP_005932.2	P51512-1
MMP16	XM_024447154.2 link	c.295-74C>T		intron_variant	Intron 3 of 6		XP_024302922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMP16	ENST00000286614.11 link	c.1084-74C>T		intron_variant	Intron 6 of 9	1	NM_005941.5	ENSP00000286614.6		P51512-1
MMP16	ENST00000544227.5 link	n.1084-74C>T		intron_variant	Intron 6 of 7	1

Frequencies

GnomAD3 genomes

AF:

0.0495

AC:

7528

AN:

152054

Hom.:

293

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0203

Gnomad AMI

AF:

0.0231

Gnomad AMR

AF:

0.0323

Gnomad ASJ

AF:

0.0300

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.0692

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0491

Gnomad OTH

AF:

0.0522

GnomAD4 exome

AF:

0.0558

AC:

75617

AN:

1353940

Hom.:

2774

AF XY:

0.0563

AC XY:

37752

AN XY:

671068

show subpopulations

African (AFR)

AF:

0.0193

AC:

574

AN:

29708

American (AMR)

AF:

0.0261

AC:

850

AN:

32526

Ashkenazi Jewish (ASJ)

AF:

0.0320

AC:

703

AN:

21992

East Asian (EAS)

AF:

0.191

AC:

7294

AN:

38102

South Asian (SAS)

AF:

0.0651

AC:

4902

AN:

75266

European-Finnish (FIN)

AF:

0.109

AC:

5514

AN:

50740

Middle Eastern (MID)

AF:

0.0494

AC:

264

AN:

5346

European-Non Finnish (NFE)

AF:

0.0498

AC:

52036

AN:

1044370

Other (OTH)

AF:

0.0623

AC:

3480

AN:

55890

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3323

6647

9970

13294

16617

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2034

4068

6102

8136

10170

<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:

0.0494

AC:

7523

AN:

152174

Hom.:

292

Cov.:

AF XY:

0.0526

AC XY:

3913

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.0202

AC:

841

AN:

41550

American (AMR)

AF:

0.0324

AC:

494

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.0300

AC:

104

AN:

3470

East Asian (EAS)

AF:

0.205

AC:

1057

AN:

5160

South Asian (SAS)

AF:

0.0690

AC:

333

AN:

4824

European-Finnish (FIN)

AF:

0.114

AC:

1205

AN:

10582

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0491

AC:

3342

AN:

68012

Other (OTH)

AF:

0.0535

AC:

113

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

365

729

1094

1458

1823

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0502

Hom.:

403

Bravo

AF:

0.0423

Asia WGS

AF:

0.145

AC:

502

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.29

(source)

DANN

Benign

0.66

PhyloP100

-0.68

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