rs149988025
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_006785.4(MALT1):āc.677A>Gā(p.Lys226Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000779 in 1,596,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. K226K) has been classified as Likely benign.
Frequency
Consequence
NM_006785.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MALT1 | NM_006785.4 | c.677A>G | p.Lys226Arg | missense_variant | 5/17 | ENST00000649217.2 | |
LOC105372146 | XR_935537.3 | n.62-12138T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MALT1 | ENST00000649217.2 | c.677A>G | p.Lys226Arg | missense_variant | 5/17 | NM_006785.4 | P3 | ||
ENST00000588835.1 | n.57-12138T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000920 AC: 140AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000764 AC: 184AN: 240832Hom.: 0 AF XY: 0.000691 AC XY: 90AN XY: 130188
GnomAD4 exome AF: 0.000764 AC: 1104AN: 1444530Hom.: 0 Cov.: 31 AF XY: 0.000825 AC XY: 592AN XY: 717872
GnomAD4 genome AF: 0.000919 AC: 140AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.000779 AC XY: 58AN XY: 74462
ClinVar
Submissions by phenotype
Combined immunodeficiency due to MALT1 deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at