chr8-88078472-G-T

Position:

• chr8-88078472-G-T

Variant summary

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

The NM_005941.5(MMP16):​c.1084-3729C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,972 control chromosomes in the GnomAD database, including 6,341 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 0.28 (6341 hom., cov: 32)
• Consequence: MMP16 NM_005941.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

MMP16 (HGNC:7162): (matrix metallopeptidase 16) 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. The encoded protein activates MMP2 by cleavage. This gene was once referred to as MT-MMP2, but was renamed as MT-MMP3 or MMP16. [provided by RefSeq, Oct 2010]

MMP16 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MMP16	NM_005941.5	c.1084-3729C>A		intron_variant		ENST00000286614.11	NP_005932.2
MMP16	XM_024447154.2	c.295-3729C>A		intron_variant			XP_024302922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MMP16	ENST00000286614.11	c.1084-3729C>A		intron_variant		1	NM_005941.5	ENSP00000286614.6
MMP16	ENST00000544227.5	n.1084-3729C>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42052 AN: 151854 Hom.: 6338 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.277 AC: 42075 AN: 151972 Hom.: 6341 Cov.: 32 AF XY: 0.272 AC XY: 20165 AN XY: 74260

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.262

Alfa AF: 0.243 Hom.: 1025

Bravo AF: 0.270

Asia WGS AF: 0.214 AC: 747 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	1.5
DANN	Benign	0.42

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: rs10504852; hg19: chr8-89090700;