Genetic Variant MMP8:c.102+72G>A (chr11-102724682-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002424.3(MMP8):c.102+72G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 1,314,524 control chromosomes in the GnomAD database, including 42,030 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 0.18 ( 3069 hom., cov: 33)

Exomes 𝑓: 0.25 ( 38961 hom. )

Consequence

MMP8
NM_002424.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

Publications

25 publications found

Variant links:

Genes affected

MMP8 (HGNC:7175): (matrix metallopeptidase 8) This gene encodes a member of the matrix metalloproteinase (MMP) family of proteins. These proteins are involved in the breakdown of extracellular matrix in embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Proteolysis at different sites on this protein results in multiple active forms of the enzyme with distinct N-termini. This protein functions in the degradation of type I, II and III collagens. The gene is part of a cluster of MMP genes which localize to chromosome 11q22.3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

MMP8 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMP8	NM_002424.3 link	c.102+72G>A		intron_variant	Intron 1 of 9	ENST00000236826.8	NP_002415.1	P22894

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMP8	ENST00000236826.8 link	c.102+72G>A		intron_variant	Intron 1 of 9	1	NM_002424.3	ENSP00000236826.3		P22894

Frequencies

GnomAD3 genomes

AF:

0.179

AC:

27180

AN:

152030

Hom.:

3066

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0473

Gnomad AMI

AF:

0.224

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.183

Gnomad EAS

AF:

0.0924

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.173

GnomAD4 exome

AF:

0.252

AC:

293140

AN:

1162374

Hom.:

38961

AF XY:

0.250

AC XY:

143827

AN XY:

576010

show subpopulations

African (AFR)

AF:

0.0369

AC:

940

AN:

25492

American (AMR)

AF:

0.216

AC:

6288

AN:

29062

Ashkenazi Jewish (ASJ)

AF:

0.179

AC:

3428

AN:

19100

East Asian (EAS)

AF:

0.0764

AC:

2638

AN:

34550

South Asian (SAS)

AF:

0.164

AC:

9557

AN:

58228

European-Finnish (FIN)

AF:

0.259

AC:

11857

AN:

45754

Middle Eastern (MID)

AF:

0.131

AC:

614

AN:

4700

European-Non Finnish (NFE)

AF:

0.275

AC:

246950

AN:

897914

Other (OTH)

AF:

0.228

AC:

10868

AN:

47574

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.526

Heterozygous variant carriers

10142

20284

30427

40569

50711

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8486

16972

25458

33944

42430

<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:

0.179

AC:

27182

AN:

152150

Hom.:

3069

Cov.:

AF XY:

0.177

AC XY:

13179

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0472

AC:

1961

AN:

41536

American (AMR)

AF:

0.198

AC:

3027

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.183

AC:

636

AN:

3468

East Asian (EAS)

AF:

0.0927

AC:

480

AN:

5180

South Asian (SAS)

AF:

0.150

AC:

725

AN:

4824

European-Finnish (FIN)

AF:

0.235

AC:

2481

AN:

10578

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.254

AC:

17265

AN:

67976

Other (OTH)

AF:

0.171

AC:

360

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1112

2224

3337

4449

5561

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

298

596

894

1192

1490

<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:

0.232

Hom.:

2334

Bravo

AF:

0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.39

(source)

DANN

Benign

0.23

PhyloP100

-1.2

PromoterAI

-0.014

Neutral

(source)

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