rs5029947
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001270508.2(TNFAIP3):c.487-8C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00405 in 1,613,456 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001270508.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFAIP3 | NM_001270508.2 | c.487-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000612899.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFAIP3 | ENST00000612899.5 | c.487-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001270508.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0148 AC: 2249AN: 152058Hom.: 37 Cov.: 33
GnomAD3 exomes AF: 0.00511 AC: 1282AN: 250862Hom.: 19 AF XY: 0.00402 AC XY: 545AN XY: 135582
GnomAD4 exome AF: 0.00293 AC: 4275AN: 1461280Hom.: 57 Cov.: 32 AF XY: 0.00272 AC XY: 1978AN XY: 726944
GnomAD4 genome ? AF: 0.0148 AC: 2254AN: 152176Hom.: 38 Cov.: 33 AF XY: 0.0142 AC XY: 1056AN XY: 74408
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Autoinflammatory syndrome, familial, Behcet-like 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at