rs56142402
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006785.4(MALT1):c.-84G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 926,772 control chromosomes in the GnomAD database, including 1,126 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.034 ( 120 hom., cov: 33)
Exomes 𝑓: 0.048 ( 1006 hom. )
Consequence
MALT1
NM_006785.4 5_prime_UTR
NM_006785.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.422
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 made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 18-58671560-G-A is Benign according to our data. Variant chr18-58671560-G-A is described in ClinVar as [Benign]. Clinvar id is 403068.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0511 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MALT1 | NM_006785.4 | c.-84G>A | 5_prime_UTR_variant | 1/17 | ENST00000649217.2 | ||
MALT1-AS1 | NR_164150.1 | n.314C>T | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MALT1 | ENST00000649217.2 | c.-84G>A | 5_prime_UTR_variant | 1/17 | NM_006785.4 | P3 | |||
MALT1 | ENST00000345724.7 | c.-84G>A | 5_prime_UTR_variant | 1/16 | 1 | A2 | |||
MALT1-AS1 | ENST00000588144.2 | n.318C>T | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
MALT1 | ENST00000650045.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0340 AC: 5167AN: 151806Hom.: 121 Cov.: 33
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GnomAD4 exome AF: 0.0479 AC: 37146AN: 774858Hom.: 1006 Cov.: 11 AF XY: 0.0478 AC XY: 17747AN XY: 371324
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GnomAD4 genome ? AF: 0.0340 AC: 5162AN: 151914Hom.: 120 Cov.: 33 AF XY: 0.0331 AC XY: 2462AN XY: 74272
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at