NM_022122.3:c.103-233T>C

Variant names:

• chr11-102705008-A-G
• rs11225388
• NM_022122.3:c.103-233T>C

Variant summary

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

The NM_022122.3(MMP27):​c.103-233T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,228 control chromosomes in the GnomAD database, including 3,134 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 0.18 (3134 hom., cov: 32)
• Consequence: MMP27 NM_022122.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

Genes affected

MMP27 (HGNC:14250): (matrix metallopeptidase 27) Proteins of the matrix metalloproteinase (MMP) 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. Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMP27	NM_022122.3	c.103-233T>C		intron_variant	Intron 1 of 9	ENST00000260229.5	NP_071405.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMP27	ENST00000260229.5	c.103-233T>C		intron_variant	Intron 1 of 9	1	NM_022122.3	ENSP00000260229.4

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27178 AN: 152110 Hom.: 3131 Cov.: 32

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0917

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.179 AC: 27177 AN: 152228 Hom.: 3134 Cov.: 32 AF XY: 0.177 AC XY: 13178 AN XY: 74400

Gnomad4 AFR AF: 0.0470

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.0919

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.160

Alfa AF: 0.230 Hom.: 5808

Bravo AF: 0.172

Asia WGS AF: 0.106 AC: 370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.9
DANN	Benign	0.31

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

Other links and lift over

dbSNP: rs11225388; hg19: chr11-102575739;