Variant rs17860949 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.336C>T(p.His112His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,613,780 control chromosomes in the GnomAD database, including 13,421 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 0.12 ( 1197 hom., cov: 33)

Exomes 𝑓: 0.13 ( 12224 hom. )

Consequence

MMP10
NM_002425.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.758

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=-0.8).

BP7

Synonymous conserved (PhyloP=-0.758 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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.336C>T	p.His112His	synonymous_variant	2/10	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.336C>T	p.His112His	synonymous_variant	2/10	1	NM_002425.3	ENSP00000279441.4	P09238
MMP10	ENST00000539681.1 linkuse as main transcript	c.336C>T	p.His112His	synonymous_variant	2/4	3		ENSP00000441485.1	F5GYX7
WTAPP1	ENST00000371455.7 linkuse as main transcript	n.325-18509G>A		intron_variant		4

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18997

AN:

152062

Hom.:

1193

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.0865

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.0773

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.0976

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.112

GnomAD3 exomes

AF:

0.114

AC:

28533

AN:

251084

Hom.:

1710

AF XY:

0.117

AC XY:

15903

AN XY:

135708

show subpopulations

Gnomad AFR exome

AF:

0.143

Gnomad AMR exome

AF:

0.0594

Gnomad ASJ exome

AF:

0.0993

Gnomad EAS exome

AF:

0.0822

Gnomad SAS exome

AF:

0.137

Gnomad FIN exome

AF:

0.0960

Gnomad NFE exome

AF:

0.129

Gnomad OTH exome

AF:

0.122

GnomAD4 exome

AF:

0.127

AC:

185535

AN:

1461600

Hom.:

12224

Cov.:

AF XY:

0.127

AC XY:

92678

AN XY:

727112

show subpopulations

Gnomad4 AFR exome

AF:

0.144

Gnomad4 AMR exome

AF:

0.0634

Gnomad4 ASJ exome

AF:

0.102

Gnomad4 EAS exome

AF:

0.0552

Gnomad4 SAS exome

AF:

0.140

Gnomad4 FIN exome

AF:

0.0977

Gnomad4 NFE exome

AF:

0.133

Gnomad4 OTH exome

AF:

0.126

GnomAD4 genome

AF:

0.125

AC:

19011

AN:

152180

Hom.:

1197

Cov.:

AF XY:

0.122

AC XY:

9046

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.0863

Gnomad4 ASJ

AF:

0.111

Gnomad4 EAS

AF:

0.0775

Gnomad4 SAS

AF:

0.138

Gnomad4 FIN

AF:

0.0976

Gnomad4 NFE

AF:

0.131

Gnomad4 OTH

AF:

0.111

Alfa

AF:

0.128

Hom.:

658

Bravo

AF:

0.124

Asia WGS

AF:

0.109

AC:

380

AN:

3478

EpiCase

AF:

0.125

EpiControl

AF:

0.132

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.5

DANN

Benign

0.68

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