11-102530930-T-C

Variant names:

• chr11-102530930-T-C
• rs11568818
• NM_002423.5:c.-230A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_002423.5(MMP7):​c.-230A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,990 control chromosomes in the GnomAD database, including 14,149 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 0.43 (14149 hom., cov: 31)
• Consequence: MMP7 NM_002423.5 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11
• Publications: 243 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002423.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MMP7	NM_002423.5	MANE Select	c.-230A>G		upstream_gene	N/A	NP_002414.1	P09237

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MMP7	ENST00000260227.5	TSL:1 MANE Select	c.-230A>G		upstream_gene	N/A	ENSP00000260227.4	P09237
	MMP7	ENST00000896702.1		c.-230A>G		upstream_gene	N/A	ENSP00000566761.1
	MMP7	ENST00000896703.1		c.-230A>G		upstream_gene	N/A	ENSP00000566762.1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64634 AN: 151874 Hom.: 14140 Cov.: 31

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.0749

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.425

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.426 AC: 64674 AN: 151990 Hom.: 14149 Cov.: 31 AF XY: 0.424 AC XY: 31481 AN XY: 74288

African (AFR) AF: 0.450 AC: 18641 AN: 41426

American (AMR) AF: 0.361 AC: 5522 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1445 AN: 3468

East Asian (EAS) AF: 0.0747 AC: 387 AN: 5182

South Asian (SAS) AF: 0.433 AC: 2088 AN: 4818

European-Finnish (FIN) AF: 0.426 AC: 4491 AN: 10548

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30478 AN: 67948

Other (OTH) AF: 0.420 AC: 886 AN: 2112

Alfa AF: 0.438 Hom.: 47473

Bravo AF: 0.421

Asia WGS AF: 0.288 AC: 1001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	17
DANN	Benign	0.87
PhyloP100		2.1
PromoterAI		0.018	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11568818; hg19: chr11-102401661;