1-1634254-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The ENST00000378675.7(MMP23B):c.991C>T(p.Gln331*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000091 ( 1 hom., cov: 10)
Exomes 𝑓: 0.00031 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MMP23B
ENST00000378675.7 stop_gained
ENST00000378675.7 stop_gained
Scores
2
5
Clinical Significance
Conservation
PhyloP100: 1.75
Genes affected
MMP23B (HGNC:7171): (matrix metallopeptidase 23B) This gene (MMP23B) encodes a member of the matrix metalloproteinase (MMP) family, and it is part of a duplicated region of chromosome 1p36.3. 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. This gene belongs to the more telomeric copy of the duplicated region. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
Variant 1-1634254-C-T is Benign according to our data. Variant chr1-1634254-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2638049.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MMP23B | NM_006983.2 | c.924C>T | p.Thr308Thr | synonymous_variant | Exon 7 of 8 | ENST00000356026.10 | NP_008914.1 | |
MMP23B | XM_047432837.1 | c.924C>T | p.Thr308Thr | synonymous_variant | Exon 7 of 8 | XP_047288793.1 | ||
MMP23B | XM_047432838.1 | c.924C>T | p.Thr308Thr | synonymous_variant | Exon 7 of 8 | XP_047288794.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 7AN: 77174Hom.: 1 Cov.: 10 FAILED QC
GnomAD3 genomes
AF:
AC:
7
AN:
77174
Hom.:
Cov.:
10
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00655 AC: 349AN: 53274Hom.: 18 AF XY: 0.00723 AC XY: 207AN XY: 28640
GnomAD3 exomes
AF:
AC:
349
AN:
53274
Hom.:
AF XY:
AC XY:
207
AN XY:
28640
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000308 AC: 152AN: 493404Hom.: 0 Cov.: 6 AF XY: 0.000361 AC XY: 95AN XY: 262920
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
152
AN:
493404
Hom.:
Cov.:
6
AF XY:
AC XY:
95
AN XY:
262920
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000907 AC: 7AN: 77172Hom.: 1 Cov.: 10 AF XY: 0.000137 AC XY: 5AN XY: 36454
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
7
AN:
77172
Hom.:
Cov.:
10
AF XY:
AC XY:
5
AN XY:
36454
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ExAC
AF:
AC:
89
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
MMP23B: BS2 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at