rs112002462
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP4_StrongBP6BS2
The NM_003184.4(TAF2):āc.157A>Gā(p.Ile53Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00153 in 1,607,978 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003184.4 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 |
---|---|---|---|---|---|---|---|
TAF2 | NM_003184.4 | c.157A>G | p.Ile53Val | missense_variant | 3/26 | ENST00000378164.7 | |
TAF2 | XM_006716621.4 | c.157A>G | p.Ile53Val | missense_variant | 3/27 | ||
TAF2 | XM_011517259.3 | c.157A>G | p.Ile53Val | missense_variant | 3/26 | ||
TAF2 | XM_017013779.3 | c.157A>G | p.Ile53Val | missense_variant | 3/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAF2 | ENST00000378164.7 | c.157A>G | p.Ile53Val | missense_variant | 3/26 | 1 | NM_003184.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00117 AC: 178AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00101 AC: 250AN: 247548Hom.: 1 AF XY: 0.000939 AC XY: 126AN XY: 134208
GnomAD4 exome AF: 0.00157 AC: 2286AN: 1455676Hom.: 4 Cov.: 31 AF XY: 0.00153 AC XY: 1105AN XY: 724538
GnomAD4 genome ? AF: 0.00117 AC: 178AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.00111 AC XY: 83AN XY: 74490
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | TAF2: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 22, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jun 15, 2022 | Variant summary: TAF2 c.157A>G (p.Ile53Val) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.001 in 247548 control chromosomes in the gnomAD database, predominantly within the Non-Finnish European subpopulation at a frequency of 0.0018, including 1 homozygote. To our knowledge, no occurrence of c.157A>G in individuals affected with Microcephaly-Thin Corpus Callosum-Intellectual Disability Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Four submitters have provided clinical-significance assessments for this variant in ClinVar after 2014 without evidence for independent evaluation, and classified the variant as VUS (n=3) or likely benign (n=1). Based on the evidence outlined above, the variant was classified as likely benign. - |
Microcephaly-thin corpus callosum-intellectual disability syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Apr 27, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at