Genetic Variant NM_022122.3:c.-23G>T (chr11-102705737-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022122.3(MMP27):c.-23G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 1,545,296 control chromosomes in the GnomAD database, including 47,193 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 ( 3122 hom., cov: 31)

Exomes 𝑓: 0.24 ( 44071 hom. )

Consequence

MMP27
NM_022122.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0610

Publications

17 publications found

Variant links:

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]

MMP27 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

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 link	c.-23G>T		5_prime_UTR_variant	Exon 1 of 10	ENST00000260229.5	NP_071405.2	Q9H306

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMP27	ENST00000260229.5 link	c.-23G>T		5_prime_UTR_variant	Exon 1 of 10	1	NM_022122.3	ENSP00000260229.4		Q9H306

Frequencies

GnomAD3 genomes

AF:

0.179

AC:

27141

AN:

151916

Hom.:

3119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0471

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.0913

Gnomad SAS

AF:

0.149

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.161

GnomAD2 exomes

AF:

0.209

AC:

48783

AN:

233640

AF XY:

0.210

show subpopulations

Gnomad AFR exome

AF:

0.0431

Gnomad AMR exome

AF:

0.227

Gnomad ASJ exome

AF:

0.181

Gnomad EAS exome

AF:

0.0961

Gnomad FIN exome

AF:

0.261

Gnomad NFE exome

AF:

0.247

Gnomad OTH exome

AF:

0.194

GnomAD4 exome

AF:

0.244

AC:

339509

AN:

1393262

Hom.:

44071

Cov.:

AF XY:

0.241

AC XY:

167944

AN XY:

695738

show subpopulations

African (AFR)

AF:

0.0356

AC:

1111

AN:

31180

American (AMR)

AF:

0.217

AC:

8714

AN:

40232

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

4516

AN:

25516

East Asian (EAS)

AF:

0.0765

AC:

2946

AN:

38510

South Asian (SAS)

AF:

0.166

AC:

13379

AN:

80676

European-Finnish (FIN)

AF:

0.267

AC:

14204

AN:

53248

Middle Eastern (MID)

AF:

0.124

AC:

699

AN:

5650

European-Non Finnish (NFE)

AF:

0.265

AC:

281139

AN:

1060294

Other (OTH)

AF:

0.221

AC:

12801

AN:

57956

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

11614

23228

34843

46457

58071

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9256

18512

27768

37024

46280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.179

AC:

27140

AN:

152034

Hom.:

3122

Cov.:

AF XY:

0.177

AC XY:

13164

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.0470

AC:

1950

AN:

41478

American (AMR)

AF:

0.191

AC:

2911

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.179

AC:

622

AN:

3466

East Asian (EAS)

AF:

0.0915

AC:

474

AN:

5178

South Asian (SAS)

AF:

0.149

AC:

718

AN:

4814

European-Finnish (FIN)

AF:

0.248

AC:

2621

AN:

10550

Middle Eastern (MID)

AF:

0.140

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.254

AC:

17260

AN:

67964

Other (OTH)

AF:

0.159

AC:

335

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1088

2175

3263

4350

5438

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.214

Hom.:

12341

Bravo

AF:

0.172

Asia WGS

AF:

0.106

AC:

370

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.4

(source)

DANN

Benign

0.72

PhyloP100

-0.061

PromoterAI

-0.021

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over