1-1634254-C-T

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

Scores

2
5

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.75
Variant links:
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
MMP23BNM_006983.2 linkc.924C>T p.Thr308Thr synonymous_variant Exon 7 of 8 ENST00000356026.10 NP_008914.1 O75900-1
MMP23BXM_047432837.1 linkc.924C>T p.Thr308Thr synonymous_variant Exon 7 of 8 XP_047288793.1
MMP23BXM_047432838.1 linkc.924C>T p.Thr308Thr synonymous_variant Exon 7 of 8 XP_047288794.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MMP23BENST00000356026.10 linkc.924C>T p.Thr308Thr synonymous_variant Exon 7 of 8 1 NM_006983.2 ENSP00000348308.5 O75900-1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
7
AN:
77174
Hom.:
1
Cov.:
10
FAILED QC
Gnomad AFR
AF:
0.000134
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000222
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000757
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00655
AC:
349
AN:
53274
Hom.:
18
AF XY:
0.00723
AC XY:
207
AN XY:
28640
show subpopulations
Gnomad AFR exome
AF:
0.00128
Gnomad AMR exome
AF:
0.00294
Gnomad ASJ exome
AF:
0.00181
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00907
Gnomad FIN exome
AF:
0.00693
Gnomad NFE exome
AF:
0.0107
Gnomad OTH exome
AF:
0.00443
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000308
AC:
152
AN:
493404
Hom.:
0
Cov.:
6
AF XY:
0.000361
AC XY:
95
AN XY:
262920
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000748
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000398
Gnomad4 FIN exome
AF:
0.000241
Gnomad4 NFE exome
AF:
0.000391
Gnomad4 OTH exome
AF:
0.000113
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000907
AC:
7
AN:
77172
Hom.:
1
Cov.:
10
AF XY:
0.000137
AC XY:
5
AN XY:
36454
show subpopulations
Gnomad4 AFR
AF:
0.000134
Gnomad4 AMR
AF:
0.000222
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000758
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000253
Hom.:
0
ExAC
AF:
0.00778
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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.55
T
BayesDel_noAF
Benign
-0.56
CADD
Benign
9.6
DANN
Uncertain
0.99
Eigen
Benign
-0.13
Eigen_PC
Benign
-0.19
FATHMM_MKL
Uncertain
0.91
D
Vest4
0.22
GERP RS
0.43

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.

Other links and lift over

dbSNP: rs569520207; hg19: chr1-1569633; API