rs652921
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001292034.3(TAB2):c.2073G>A(p.Arg691=) variant causes a synonymous change. The variant allele was found at a frequency of 0.124 in 1,613,838 control chromosomes in the GnomAD database, including 17,682 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.12 ( 1723 hom., cov: 32)
Exomes 𝑓: 0.12 ( 15959 hom. )
Consequence
TAB2
NM_001292034.3 synonymous
NM_001292034.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.94
Genes affected
TAB2 (HGNC:17075): (TGF-beta activated kinase 1 (MAP3K7) binding protein 2) The protein encoded by this gene is an activator of MAP3K7/TAK1, which is required for for the IL-1 induced activation of nuclear factor kappaB and MAPK8/JNK. This protein forms a kinase complex with TRAF6, MAP3K7 and TAB1, and it thus serves as an adaptor that links MAP3K7 and TRAF6. This protein, along with TAB1 and MAP3K7, also participates in the signal transduction induced by TNFSF11/RANKl through the activation of the receptor activator of NF-kappaB (TNFRSF11A/RANK), which may regulate the development and function of osteoclasts. Studies of the related mouse protein indicate that it functions to protect against liver damage caused by chemical stressors. Mutations in this gene cause congenital heart defects, multiple types, 2 (CHTD2). Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
?
Variant 6-149409710-G-A is Benign according to our data. Variant chr6-149409710-G-A is described in ClinVar as [Benign]. Clinvar id is 1241569.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAB2 | NM_001292034.3 | c.2073G>A | p.Arg691= | synonymous_variant | 7/7 | ENST00000637181.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAB2 | ENST00000637181.2 | c.2073G>A | p.Arg691= | synonymous_variant | 7/7 | 1 | NM_001292034.3 | P1 | |
TAB2 | ENST00000470466.5 | c.*672G>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 1 | ||||
TAB2 | ENST00000367456.5 | c.2073G>A | p.Arg691= | synonymous_variant | 8/8 | 5 | P1 | ||
TAB2 | ENST00000636456.1 | c.1221G>A | p.Arg407= | synonymous_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.121 AC: 18467AN: 152022Hom.: 1721 Cov.: 32
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GnomAD3 exomes AF: 0.179 AC: 44952AN: 251346Hom.: 6139 AF XY: 0.174 AC XY: 23602AN XY: 135836
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GnomAD4 exome AF: 0.125 AC: 182306AN: 1461698Hom.: 15959 Cov.: 32 AF XY: 0.126 AC XY: 91640AN XY: 727150
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GnomAD4 genome ? AF: 0.121 AC: 18476AN: 152140Hom.: 1723 Cov.: 32 AF XY: 0.128 AC XY: 9482AN XY: 74356
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 04, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at