Variant 11-102790545-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_002421.4(MMP1):c.1301-24A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 1,422,984 control chromosomes in the GnomAD database, including 3,158 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 0.061 ( 634 hom., cov: 33)

Exomes 𝑓: 0.029 ( 2524 hom. )

Consequence

MMP1
NM_002421.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0480

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:):

WTAPP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 11-102790545-T-G is Benign according to our data. Variant chr11-102790545-T-G is described in ClinVar as [Benign]. Clinvar id is 1260456.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
MMP1	NM_002421.4 linkuse as main transcript	c.1301-24A>C	intron_variant	ENST00000315274.7	NP_002412.1	P03956Q53G95
MMP1	NM_001145938.2 linkuse as main transcript	c.1103-24A>C	intron_variant		NP_001139410.1	B4DN15
WTAPP1	NR_038390.1 linkuse as main transcript	n.390-2600T>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MMP1	ENST00000315274.7 linkuse as main transcript	c.1301-24A>C		intron_variant		1	NM_002421.4	ENSP00000322788.6		P03956

Frequencies

GnomAD3 genomes

AF:

0.0605

AC:

9203

AN:

152162

Hom.:

630

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.0680

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.0541

Gnomad EAS

AF:

0.245

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.00103

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.00964

Gnomad OTH

AF:

0.0659

GnomAD3 exomes

AF:

0.0691

AC:

14959

AN:

216484

Hom.:

1202

AF XY:

0.0630

AC XY:

7370

AN XY:

117022

show subpopulations

Gnomad AFR exome

AF:

0.121

Gnomad AMR exome

AF:

0.161

Gnomad ASJ exome

AF:

0.0465

Gnomad EAS exome

AF:

0.258

Gnomad SAS exome

AF:

0.0956

Gnomad FIN exome

AF:

0.000983

Gnomad NFE exome

AF:

0.0110

Gnomad OTH exome

AF:

0.0488

GnomAD4 exome

AF:

0.0294

AC:

37404

AN:

1270704

Hom.:

2524

Cov.:

AF XY:

0.0305

AC XY:

19482

AN XY:

639520

show subpopulations

Gnomad4 AFR exome

AF:

0.116

Gnomad4 AMR exome

AF:

0.152

Gnomad4 ASJ exome

AF:

0.0438

Gnomad4 EAS exome

AF:

0.243

Gnomad4 SAS exome

AF:

0.0887

Gnomad4 FIN exome

AF:

0.00151

Gnomad4 NFE exome

AF:

0.00844

Gnomad4 OTH exome

AF:

0.0438

GnomAD4 genome

AF:

0.0605

AC:

9216

AN:

152280

Hom.:

634

Cov.:

AF XY:

0.0633

AC XY:

4710

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.112

Gnomad4 AMR

AF:

0.111

Gnomad4 ASJ

AF:

0.0541

Gnomad4 EAS

AF:

0.245

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.00103

Gnomad4 NFE

AF:

0.00964

Gnomad4 OTH

AF:

0.0747

Alfa

AF:

0.0188

Hom.:

Bravo

AF:

0.0711

Asia WGS

AF:

0.194

AC:

673

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	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.91

BranchPoint Hunter

2.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.21

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.21

Position offset: -3

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