Variant 11-102779223-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002425.3(MMP10):c.486T>C(p.Phe162Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 1,612,926 control chromosomes in the GnomAD database, including 4,471 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 0.097 ( 1023 hom., cov: 33)

Exomes 𝑓: 0.063 ( 3448 hom. )

Consequence

MMP10
NM_002425.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.41

Variant links:

Genes affected

MMP10 (HGNC:7156): (matrix metallopeptidase 10) This gene encodes a member of the peptidase M10 family of matrix metalloproteinases (MMPs). Proteins in this 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. The encoded preproprotein is proteolytically processed to generate the mature protease. This secreted protease breaks down fibronectin, laminin, elastin, proteoglycan core protein, gelatins, and several types of collagen. The gene is part of a cluster of MMP genes on chromosome 11. [provided by RefSeq, Jan 2016]

MMP10 links:

WTAPP1 (HGNC:):

WTAPP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP7

Synonymous conserved (PhyloP=1.41 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MMP10	NM_002425.3 linkuse as main transcript	c.486T>C	p.Phe162Phe	synonymous_variant	3/10	ENST00000279441.9	NP_002416.1	P09238

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MMP10	ENST00000279441.9 linkuse as main transcript	c.486T>C	p.Phe162Phe	synonymous_variant	3/10	1	NM_002425.3	ENSP00000279441.4	P09238
MMP10	ENST00000539681.1 linkuse as main transcript	c.486T>C	p.Phe162Phe	synonymous_variant	3/4	3		ENSP00000441485.1	F5GYX7
WTAPP1	ENST00000371455.7 linkuse as main transcript	n.325-18801A>G		intron_variant		4

Frequencies

GnomAD3 genomes

AF:

0.0967

AC:

14710

AN:

152166

Hom.:

1022

Cov.:

show subpopulations

Gnomad AFR

AF:

0.190

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0897

Gnomad ASJ

AF:

0.0858

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.0236

Gnomad FIN

AF:

0.0342

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0652

Gnomad OTH

AF:

0.106

GnomAD3 exomes

AF:

0.0612

AC:

15377

AN:

251094

Hom.:

717

AF XY:

0.0589

AC XY:

7987

AN XY:

135696

show subpopulations

Gnomad AFR exome

AF:

0.196

Gnomad AMR exome

AF:

0.0447

Gnomad ASJ exome

AF:

0.0925

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0255

Gnomad FIN exome

AF:

0.0354

Gnomad NFE exome

AF:

0.0685

Gnomad OTH exome

AF:

0.0655

GnomAD4 exome

AF:

0.0625

AC:

91321

AN:

1460642

Hom.:

3448

Cov.:

AF XY:

0.0614

AC XY:

44616

AN XY:

726668

show subpopulations

Gnomad4 AFR exome

AF:

0.195

Gnomad4 AMR exome

AF:

0.0493

Gnomad4 ASJ exome

AF:

0.0943

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0263

Gnomad4 FIN exome

AF:

0.0352

Gnomad4 NFE exome

AF:

0.0642

Gnomad4 OTH exome

AF:

0.0686

GnomAD4 genome

AF:

0.0967

AC:

14732

AN:

152284

Hom.:

1023

Cov.:

AF XY:

0.0940

AC XY:

6999

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.190

Gnomad4 AMR

AF:

0.0896

Gnomad4 ASJ

AF:

0.0858

Gnomad4 EAS

AF:

0.000385

Gnomad4 SAS

AF:

0.0238

Gnomad4 FIN

AF:

0.0342

Gnomad4 NFE

AF:

0.0652

Gnomad4 OTH

AF:

0.104

Alfa

AF:

0.0796

Hom.:

286

Bravo

AF:

0.105

Asia WGS

AF:

0.0220

AC:

AN:

3478

EpiCase

AF:

0.0712

EpiControl

AF:

0.0699

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

1.0

DANN

Benign

0.55

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over