Variant chr11-102716423-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_002424.3(MMP8):c.785-4C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00018 ( 0 hom., cov: 12)

Exomes 𝑓: 0.0015 ( 0 hom. )

Consequence

MMP8
NM_002424.3 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00002312

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.515

Variant links:

Genes affected

MMP8 (HGNC:7175): (matrix metallopeptidase 8) This gene encodes a member of the matrix metalloproteinase (MMP) family of proteins. These proteins are involved in the breakdown of extracellular matrix in embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Proteolysis at different sites on this protein results in multiple active forms of the enzyme with distinct N-termini. This protein functions in the degradation of type I, II and III collagens. The gene is part of a cluster of MMP genes which localize to chromosome 11q22.3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

MMP8 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 11-102716423-G-A is Benign according to our data. Variant chr11-102716423-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 724355.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MMP8	NM_002424.3 linkuse as main transcript	c.785-4C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000236826.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
MMP8	ENST00000236826.8 linkuse as main transcript	c.785-4C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1	NM_002424.3	P1
MMP8	ENST00000438475.2 linkuse as main transcript	c.711-4C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	5
MMP8	ENST00000528662.6 linkuse as main transcript	c.*762-4C>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.000183

AC:

AN:

87666

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000952

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000525

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000491

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000148

Gnomad OTH

AF:

0.00169

GnomAD4 exome

AF:

0.00148

AC:

455

AN:

307606

Hom.:

Cov.:

AF XY:

0.00151

AC XY:

253

AN XY:

167934

show subpopulations

Gnomad4 AFR exome

AF:

0.00116

Gnomad4 AMR exome

AF:

0.00118

Gnomad4 ASJ exome

AF:

0.00174

Gnomad4 EAS exome

AF:

0.00156

Gnomad4 SAS exome

AF:

0.00223

Gnomad4 FIN exome

AF:

0.000544

Gnomad4 NFE exome

AF:

0.00148

Gnomad4 OTH exome

AF:

0.00154

GnomAD4 genome

AF:

0.000183

AC:

AN:

87646

Hom.:

Cov.:

AF XY:

0.000201

AC XY:

AN XY:

39766

show subpopulations

Gnomad4 AFR

AF:

0.0000952

Gnomad4 AMR

AF:

0.000525

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000491

Gnomad4 NFE

AF:

0.000148

Gnomad4 OTH

AF:

0.00169

Alfa

AF:

0.000843

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Apr 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.27

DANN

Benign

0.28

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000023

dbscSNV1_RF

Benign

0.0

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over