Variant chr11-102527862-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002423.5(MMP7):c.230G>A(p.Arg77His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,613,680 control chromosomes in the GnomAD database, including 37,027 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.16 ( 2529 hom., cov: 32)

Exomes 𝑓: 0.21 ( 34498 hom. )

Consequence

MMP7
NM_002423.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.285

Variant links:

Genes affected

MMP7 (HGNC:7174): (matrix metallopeptidase 7) 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 proteoglycans, fibronectin, elastin and casein and differs from most MMP family members in that it lacks a conserved C-terminal hemopexin domain. The enzyme is involved in wound healing, and studies in mice suggest that it regulates the activity of defensins in intestinal mucosa. The gene is part of a cluster of MMP genes on chromosome 11. This gene exhibits elevated expression levels in multiple human cancers. [provided by RefSeq, Jan 2016]

MMP7 links:

MMP7 (HGNC:):

MMP7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0057508945).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MMP7	NM_002423.5 linkuse as main transcript	c.230G>A	p.Arg77His	missense_variant	2/6	ENST00000260227.5	NP_002414.1	P09237

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MMP7	ENST00000260227.5 linkuse as main transcript	c.230G>A	p.Arg77His	missense_variant	2/6	1	NM_002423.5	ENSP00000260227.4	P09237
MMP7	ENST00000531200.1 linkuse as main transcript	n.277G>A		non_coding_transcript_exon_variant	2/3	2
MMP7	ENST00000533366.5 linkuse as main transcript	n.280G>A		non_coding_transcript_exon_variant	2/4	2

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24957

AN:

151944

Hom.:

2528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0401

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.0917

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.228

Gnomad OTH

AF:

0.177

GnomAD3 exomes

AF:

0.188

AC:

47272

AN:

251434

Hom.:

4916

AF XY:

0.187

AC XY:

25465

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.0393

Gnomad AMR exome

AF:

0.152

Gnomad ASJ exome

AF:

0.239

Gnomad EAS exome

AF:

0.255

Gnomad SAS exome

AF:

0.0937

Gnomad FIN exome

AF:

0.229

Gnomad NFE exome

AF:

0.221

Gnomad OTH exome

AF:

0.210

GnomAD4 exome

AF:

0.211

AC:

307798

AN:

1461618

Hom.:

34498

Cov.:

AF XY:

0.209

AC XY:

151721

AN XY:

727124

show subpopulations

Gnomad4 AFR exome

AF:

0.0326

Gnomad4 AMR exome

AF:

0.157

Gnomad4 ASJ exome

AF:

0.235

Gnomad4 EAS exome

AF:

0.219

Gnomad4 SAS exome

AF:

0.0970

Gnomad4 FIN exome

AF:

0.236

Gnomad4 NFE exome

AF:

0.226

Gnomad4 OTH exome

AF:

0.200

GnomAD4 genome

AF:

0.164

AC:

24962

AN:

152062

Hom.:

2529

Cov.:

AF XY:

0.161

AC XY:

11981

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.0400

Gnomad4 AMR

AF:

0.164

Gnomad4 ASJ

AF:

0.228

Gnomad4 EAS

AF:

0.233

Gnomad4 SAS

AF:

0.0924

Gnomad4 FIN

AF:

0.214

Gnomad4 NFE

AF:

0.228

Gnomad4 OTH

AF:

0.175

Alfa

AF:

0.210

Hom.:

8922

Bravo

AF:

0.156

TwinsUK

AF:

0.230

AC:

851

ALSPAC

AF:

0.231

AC:

891

ESP6500AA

AF:

0.0461

AC:

203

ESP6500EA

AF:

0.219

AC:

1884

ExAC

AF:

0.185

AC:

22492

Asia WGS

AF:

0.132

AC:

460

AN:

3478

EpiCase

AF:

0.219

EpiControl

AF:

0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.071

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.75

CADD

Benign

0.027

DANN

Benign

0.89

DEOGEN2

Benign

0.049

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.027

LIST_S2

Benign

0.094

MetaRNN

Benign

0.0058

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.74

PrimateAI

Benign

0.22

PROVEAN

Benign

-0.24

REVEL

Benign

0.069

Sift

Benign

0.15

Sift4G

Benign

0.15

Polyphen

0.012

Vest4

0.029

MPC

0.031

ClinPred

0.0031

GERP RS

-7.8

Varity_R

0.051

gMVP

0.28

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over