NM_006785.4:c.30C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_006785.4(MALT1):c.30C>T(p.Ala10Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000367 in 1,089,336 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000037 ( 0 hom. )
Consequence
MALT1
NM_006785.4 synonymous
NM_006785.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.907
Publications
0 publications found
Genes affected
MALT1 (HGNC:6819): (MALT1 paracaspase) This gene encodes a caspase-like protease that plays a role in BCL10-induced activation of NF-kappaB. The protein is a component of the CARMA1-BCL10-MALT1 (CBM) signalosome that triggers NF-kappaB signaling and lymphoctye activation following antigen-receptor stimulation. Mutations in this gene result in immunodeficiency 12 (IMD12). This gene has been found to be recurrently rearranged in chromosomal translocations with other genes in mucosa-associated lymphoid tissue lymphomas, including a t(11;18)(q21;q21) translocation with the baculoviral IAP repeat-containing protein 3 (also known as apoptosis inhibitor 2) locus [BIRC3(API2)-MALT1], and a t(14;18)(q32;q21) translocation with the immunoglobulin heavy chain locus (IGH-MALT1). Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, May 2018]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 18-58671673-C-T is Benign according to our data. Variant chr18-58671673-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1694875.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.907 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000367 AC: 4AN: 1089336Hom.: 0 Cov.: 31 AF XY: 0.00000385 AC XY: 2AN XY: 519602 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1089336
Hom.:
Cov.:
31
AF XY:
AC XY:
2
AN XY:
519602
show subpopulations
African (AFR)
AF:
AC:
0
AN:
22494
American (AMR)
AF:
AC:
0
AN:
8484
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
13938
East Asian (EAS)
AF:
AC:
0
AN:
25638
South Asian (SAS)
AF:
AC:
0
AN:
24938
European-Finnish (FIN)
AF:
AC:
0
AN:
21600
Middle Eastern (MID)
AF:
AC:
0
AN:
2874
European-Non Finnish (NFE)
AF:
AC:
4
AN:
926222
Other (OTH)
AF:
AC:
0
AN:
43148
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.513
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
MALT1: PM2:Supporting, BP4, BP7 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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
Publications
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