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GeneBe

rs17576

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PM2_SupportingBP4_Moderate

The NM_004994.3(MMP9):c.836A>C(p.Gln279Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q279R) has been classified as Benign.

Frequency

Genomes: not found (cov: 31)

Consequence

MMP9
NM_004994.3 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23

Links

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 31.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.23929572).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MMP9NM_004994.3 linkuse as main transcriptc.836A>C p.Gln279Pro missense_variant 6/13 ENST00000372330.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MMP9ENST00000372330.3 linkuse as main transcriptc.836A>C p.Gln279Pro missense_variant 6/131 NM_004994.3 P1

Frequencies

GnomAD3 genomes
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.37
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.46
Cadd
Benign
23
Dann
Uncertain
0.99
DEOGEN2
Benign
0.13
T
Eigen
Benign
0.032
Eigen_PC
Benign
-0.0083
FATHMM_MKL
Benign
0.62
D
LIST_S2
Benign
0.82
T
M_CAP
Benign
0.0078
T
MetaRNN
Benign
0.24
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.90
L
MutationTaster
Benign
0.83
N
PrimateAI
Benign
0.26
T
PROVEAN
Benign
-1.4
N
REVEL
Benign
0.12
Sift
Benign
0.20
T
Sift4G
Benign
0.16
T
Polyphen
0.94
P
Vest4
0.20
MutPred
0.56
Loss of stability (P = 0.0339);
MVP
0.63
ClinPred
0.56
D
GERP RS
2.7
Varity_R
0.20
gMVP
0.93

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17576; hg19: chr20-44640225;