Genetic Variant MMP1:c.900-34A>G (chr11-102792772-T-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002421.4(MMP1):c.900-34A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 1,594,966 control chromosomes in the GnomAD database, including 73,860 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.31 ( 8105 hom., cov: 32)

Exomes 𝑓: 0.29 ( 65755 hom. )

Consequence

MMP1
NM_002421.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.38

Variant links:

Genes affected

MMP1 (HGNC:7155): (matrix metallopeptidase 1) This gene encodes a member of the peptidase M10 family 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. The encoded preproprotein is proteolytically processed to generate the mature protease. This secreted protease breaks down the interstitial collagens, including types I, II, and III. The gene is part of a cluster of MMP genes on chromosome 11. Mutations in this gene are associated with chronic obstructive pulmonary disease (COPD). Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Jan 2016]

MMP1 links:

WTAPP1 (HGNC:44115): (WTAP pseudogene 1)

WTAPP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 0 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 11-102792772-T-C is Benign according to our data. Variant chr11-102792772-T-C is described in ClinVar as [Benign]. Clinvar id is 1293714.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
MMP1	NM_002421.4 link	c.900-34A>G	intron_variant	Intron 6 of 9	ENST00000315274.7	NP_002412.1	P03956Q53G95
MMP1	NM_001145938.2 link	c.702-34A>G	intron_variant	Intron 6 of 9		NP_001139410.1	B4DN15
WTAPP1	NR_038390.1 link	n.390-373T>C	intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMP1	ENST00000315274.7 link	c.900-34A>G		intron_variant	Intron 6 of 9	1	NM_002421.4	ENSP00000322788.6		P03956

Frequencies

GnomAD3 genomes

AF:

0.310

AC:

47168

AN:

152010

Hom.:

8079

Cov.:

show subpopulations

Gnomad AFR

AF:

0.305

Gnomad AMI

AF:

0.258

Gnomad AMR

AF:

0.417

Gnomad ASJ

AF:

0.261

Gnomad EAS

AF:

0.707

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.228

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.273

Gnomad OTH

AF:

0.321

GnomAD3 exomes

AF:

0.340

AC:

84245

AN:

247700

Hom.:

16418

AF XY:

0.332

AC XY:

44447

AN XY:

133894

show subpopulations

Gnomad AFR exome

AF:

0.311

Gnomad AMR exome

AF:

0.470

Gnomad ASJ exome

AF:

0.269

Gnomad EAS exome

AF:

0.708

Gnomad SAS exome

AF:

0.337

Gnomad FIN exome

AF:

0.232

Gnomad NFE exome

AF:

0.275

Gnomad OTH exome

AF:

0.301

GnomAD4 exome

AF:

0.292

AC:

421589

AN:

1442838

Hom.:

65755

Cov.:

AF XY:

0.292

AC XY:

209692

AN XY:

717266

show subpopulations

Gnomad4 AFR exome

AF:

0.300

Gnomad4 AMR exome

AF:

0.460

Gnomad4 ASJ exome

AF:

0.266

Gnomad4 EAS exome

AF:

0.670

Gnomad4 SAS exome

AF:

0.333

Gnomad4 FIN exome

AF:

0.236

Gnomad4 NFE exome

AF:

0.271

Gnomad4 OTH exome

AF:

0.306

GnomAD4 genome

AF:

0.310

AC:

47222

AN:

152128

Hom.:

8105

Cov.:

AF XY:

0.314

AC XY:

23379

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.305

Gnomad4 AMR

AF:

0.417

Gnomad4 ASJ

AF:

0.261

Gnomad4 EAS

AF:

0.707

Gnomad4 SAS

AF:

0.349

Gnomad4 FIN

AF:

0.228

Gnomad4 NFE

AF:

0.273

Gnomad4 OTH

AF:

0.328

Alfa

AF:

0.288

Hom.:

6953

Bravo

AF:

0.325

Asia WGS

AF:

0.495

AC:

1722

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.7

DANN

Benign

0.44

BranchPoint Hunter

0.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over