17-28342346-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_021137.5(TNFAIP1):c.618C>T(p.Asp206=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00562 in 1,607,540 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0059 ( 5 hom., cov: 32)
Exomes 𝑓: 0.0056 ( 71 hom. )
Consequence
TNFAIP1
NM_021137.5 synonymous
NM_021137.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.83
Genes affected
TNFAIP1 (HGNC:11894): (TNF alpha induced protein 1) This gene was identified as a gene whose expression can be induced by the tumor necrosis factor alpha (TNF) in umbilical vein endothelial cells. Studies of a similar gene in mouse suggest that the expression of this gene is developmentally regulated in a tissue-specific manner. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 17-28342346-C-T is Benign according to our data. Variant chr17-28342346-C-T is described in ClinVar as [Benign]. Clinvar id is 3024741.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.84 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFAIP1 | NM_021137.5 | c.618C>T | p.Asp206= | synonymous_variant | 6/7 | ENST00000226225.7 | |
TNFAIP1 | XM_017024993.3 | c.618C>T | p.Asp206= | synonymous_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFAIP1 | ENST00000226225.7 | c.618C>T | p.Asp206= | synonymous_variant | 6/7 | 1 | NM_021137.5 | P1 | |
TNFAIP1 | ENST00000544907.6 | c.306C>T | p.Asp102= | synonymous_variant | 5/6 | 2 | |||
TNFAIP1 | ENST00000577535.1 | c.306C>T | p.Asp102= | synonymous_variant | 4/4 | 3 | |||
TNFAIP1 | ENST00000583213.1 | n.339C>T | non_coding_transcript_exon_variant | 4/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00592 AC: 901AN: 152224Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.00592 AC: 1489AN: 251318Hom.: 12 AF XY: 0.00571 AC XY: 776AN XY: 135854
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GnomAD4 exome AF: 0.00559 AC: 8138AN: 1455198Hom.: 71 Cov.: 33 AF XY: 0.00571 AC XY: 4129AN XY: 722650
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GnomAD4 genome AF: 0.00591 AC: 901AN: 152342Hom.: 5 Cov.: 32 AF XY: 0.00549 AC XY: 409AN XY: 74504
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | TNFAIP1: BP4, BP7, BS1, BS2 - |
Computational scores
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BayesDel_noAF
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at