rs2176771

Variant names:

• chr8-88195036-C-A
• rs2176771
• NM_005941.5:c.281+2122G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-88195036-C-A
• chr8-88195036-C-G
• chr8-88195036-C-T

Variant summary

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

The ENST00000286614.11(MMP16):​c.281+2122G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,926 control chromosomes in the GnomAD database, including 33,594 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 0.64 (33594 hom., cov: 30)
• Consequence: MMP16 ENST00000286614.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 4 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000286614.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MMP16	NM_005941.5	MANE Select	c.281+2122G>T		intron	N/A	NP_005932.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MMP16	ENST00000286614.11	TSL:1 MANE Select	c.281+2122G>T		intron	N/A	ENSP00000286614.6
	MMP16	ENST00000544227.5	TSL:1	n.281+2122G>T		intron	N/A
	MMP16	ENST00000522726.1	TSL:4	c.332+2122G>T		intron	N/A	ENSP00000429147.1

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97686 AN: 151808 Hom.: 33603 Cov.: 30

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.643 AC: 97699 AN: 151926 Hom.: 33594 Cov.: 30 AF XY: 0.638 AC XY: 47371 AN XY: 74232

African (AFR) AF: 0.438 AC: 18128 AN: 41414

American (AMR) AF: 0.504 AC: 7694 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2380 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2201 AN: 5124

South Asian (SAS) AF: 0.630 AC: 3033 AN: 4812

European-Finnish (FIN) AF: 0.781 AC: 8260 AN: 10578

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.791 AC: 53738 AN: 67954

Other (OTH) AF: 0.634 AC: 1332 AN: 2100

Alfa AF: 0.729 Hom.: 137858

Bravo AF: 0.613

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.37
DANN	Benign	0.64
PhyloP100		-0.044
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2176771; hg19: chr8-89207265;