11-102725332-C-T

Variant names:

• chr11-102725332-C-T
• rs1320632
• ENST00000528662.6:n.-148-329G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000528662.6(MMP8):​n.-148-329G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,224 control chromosomes in the GnomAD database, including 65,115 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 0.92 (65115 hom., cov: 31)
• Consequence: MMP8 ENST00000528662.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 30 publications found

Genes affected

MMP8 (HGNC:7175): (matrix metallopeptidase 8) This gene encodes a member of the matrix metalloproteinase (MMP) family of proteins. These proteins are involved in the breakdown of extracellular matrix in embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Proteolysis at different sites on this protein results in multiple active forms of the enzyme with distinct N-termini. This protein functions in the degradation of type I, II and III collagens. The gene is part of a cluster of MMP genes which localize to chromosome 11q22.3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528662.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MMP8	ENST00000528662.6	TSL:5	n.-148-329G>A		intron	N/A	ENSP00000431431.2	E9PL87

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140628 AN: 152106 Hom.: 65057 Cov.: 31

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.925 AC: 140745 AN: 152224 Hom.: 65115 Cov.: 31 AF XY: 0.926 AC XY: 68880 AN XY: 74422

African (AFR) AF: 0.925 AC: 38420 AN: 41526

American (AMR) AF: 0.932 AC: 14265 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3092 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5167 AN: 5172

South Asian (SAS) AF: 0.940 AC: 4528 AN: 4816

European-Finnish (FIN) AF: 0.927 AC: 9829 AN: 10608

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62352 AN: 68012

Other (OTH) AF: 0.928 AC: 1963 AN: 2116

Alfa AF: 0.919 Hom.: 16152

Bravo AF: 0.926

Asia WGS AF: 0.973 AC: 3382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.42
DANN	Benign	0.22
PhyloP100		-1.2
PromoterAI		-0.046	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1320632; hg19: chr11-102596063;