rs12924764

Positions:

• chr16-55464137-G-A
• chr16-55464137-G-C
• chr16-55464137-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000570308.5(MMP2):​c.-349-415G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,066 control chromosomes in the GnomAD database, including 19,591 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 0.50 (19591 hom., cov: 33)
• Consequence: MMP2 ENST00000570308.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

Genes affected

MMP2 (HGNC:7166): (matrix metallopeptidase 2) This gene is a member of the matrix metalloproteinase (MMP) gene family, that are zinc-dependent enzymes capable of cleaving components of the extracellular matrix and molecules involved in signal transduction. The protein encoded by this gene is a gelatinase A, type IV collagenase, that contains three fibronectin type II repeats in its catalytic site that allow binding of denatured type IV and V collagen and elastin. Unlike most MMP family members, activation of this protein can occur on the cell membrane. This enzyme can be activated extracellularly by proteases, or, intracellulary by its S-glutathiolation with no requirement for proteolytical removal of the pro-domain. This protein is thought to be involved in multiple pathways including roles in the nervous system, endometrial menstrual breakdown, regulation of vascularization, and metastasis. Mutations in this gene have been associated with Winchester syndrome and Nodulosis-Arthropathy-Osteolysis (NAO) syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MMP2	ENST00000570308.5	c.-349-415G>A		intron_variant		1		ENSP00000461421

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76100 AN: 151946 Hom.: 19561 Cov.: 33

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.501 AC: 76180 AN: 152066 Hom.: 19591 Cov.: 33 AF XY: 0.506 AC XY: 37595 AN XY: 74322

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.487

Alfa AF: 0.502 Hom.: 26503

Bravo AF: 0.507

Asia WGS AF: 0.673 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12924764; hg19: chr16-55498049;