Variant chr11-102790368-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002421.4(MMP1):c.*44A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 1,185,778 control chromosomes in the GnomAD database, including 70,945 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 8955 hom., cov: 33)

Exomes 𝑓: 0.34 ( 61990 hom. )

Consequence

MMP1
NM_002421.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.215

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

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 11-102790368-T-C is Benign according to our data. Variant chr11-102790368-T-C is described in ClinVar as [Benign]. Clinvar id is 1245928.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
MMP1	NM_002421.4 linkuse as main transcript	c.*44A>G	3_prime_UTR_variant	10/10	ENST00000315274.7	NP_002412.1
WTAPP1	NR_038390.1 linkuse as main transcript	n.390-2777T>C	intron_variant, non_coding_transcript_variant
MMP1	NM_001145938.2 linkuse as main transcript	c.*44A>G	3_prime_UTR_variant	10/10		NP_001139410.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MMP1	ENST00000315274.7 linkuse as main transcript	c.*44A>G		3_prime_UTR_variant	10/10	1	NM_002421.4	ENSP00000322788	P1
WTAPP1	ENST00000371455.7 linkuse as main transcript	n.325-7656T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

51147

AN:

152012

Hom.:

8951

Cov.:

show subpopulations

Gnomad AFR

AF:

0.362

Gnomad AMI

AF:

0.286

Gnomad AMR

AF:

0.260

Gnomad ASJ

AF:

0.395

Gnomad EAS

AF:

0.0848

Gnomad SAS

AF:

0.320

Gnomad FIN

AF:

0.288

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.364

Gnomad OTH

AF:

0.324

GnomAD3 exomes

AF:

0.313

AC:

66843

AN:

213750

Hom.:

11260

AF XY:

0.317

AC XY:

36433

AN XY:

115008

show subpopulations

Gnomad AFR exome

AF:

0.356

Gnomad AMR exome

AF:

0.216

Gnomad ASJ exome

AF:

0.396

Gnomad EAS exome

AF:

0.0828

Gnomad SAS exome

AF:

0.322

Gnomad FIN exome

AF:

0.305

Gnomad NFE exome

AF:

0.364

Gnomad OTH exome

AF:

0.326

GnomAD4 exome

AF:

0.341

AC:

352787

AN:

1033648

Hom.:

61990

Cov.:

AF XY:

0.341

AC XY:

180694

AN XY:

529690

show subpopulations

Gnomad4 AFR exome

AF:

0.362

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.391

Gnomad4 EAS exome

AF:

0.117

Gnomad4 SAS exome

AF:

0.318

Gnomad4 FIN exome

AF:

0.309

Gnomad4 NFE exome

AF:

0.361

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.336

AC:

51178

AN:

152130

Hom.:

8955

Cov.:

AF XY:

0.329

AC XY:

24456

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.362

Gnomad4 AMR

AF:

0.259

Gnomad4 ASJ

AF:

0.395

Gnomad4 EAS

AF:

0.0844

Gnomad4 SAS

AF:

0.320

Gnomad4 FIN

AF:

0.288

Gnomad4 NFE

AF:

0.364

Gnomad4 OTH

AF:

0.322

Alfa

AF:

0.339

Hom.:

6801

Bravo

AF:

0.333

Asia WGS

AF:

0.232

AC:

806

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.5

DANN

Benign

0.70

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

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