chr2-161231044-T-C
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001199135.3(TANK):āc.594T>Cā(p.Ala198=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000362 in 1,614,174 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0021 ( 2 hom., cov: 33)
Exomes š: 0.00018 ( 0 hom. )
Consequence
TANK
NM_001199135.3 synonymous
NM_001199135.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.756
Genes affected
TANK (HGNC:11562): (TRAF family member associated NFKB activator) The TRAF (tumor necrosis factor receptor-associated factor) family of proteins associate with and transduce signals from members of the tumor necrosis factor receptor superfamily. The protein encoded by this gene is found in the cytoplasm and can bind to TRAF1, TRAF2, or TRAF3, thereby inhibiting TRAF function by sequestering the TRAFs in a latent state in the cytoplasm. For example, the protein encoded by this gene can block TRAF2 binding to LMP1, the Epstein-Barr virus transforming protein, and inhibit LMP1-mediated NF-kappa-B activation. Three alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 2-161231044-T-C is Benign according to our data. Variant chr2-161231044-T-C is described in ClinVar as [Benign]. Clinvar id is 711347.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.756 with no splicing effect.
BS2
High AC in GnomAd4 at 315 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TANK | NM_001199135.3 | c.594T>C | p.Ala198= | synonymous_variant | 7/8 | ENST00000392749.7 | NP_001186064.1 | |
PSMD14-DT | NR_110593.1 | n.349-7561A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TANK | ENST00000392749.7 | c.594T>C | p.Ala198= | synonymous_variant | 7/8 | 1 | NM_001199135.3 | ENSP00000376505 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00201 AC: 306AN: 152200Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000521 AC: 131AN: 251298Hom.: 0 AF XY: 0.000353 AC XY: 48AN XY: 135818
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GnomAD4 exome AF: 0.000184 AC: 269AN: 1461856Hom.: 0 Cov.: 32 AF XY: 0.000151 AC XY: 110AN XY: 727226
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GnomAD4 genome AF: 0.00207 AC: 315AN: 152318Hom.: 2 Cov.: 33 AF XY: 0.00216 AC XY: 161AN XY: 74488
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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 | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 29, 2018 | - - |
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