rs12442879
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_207037.2(TCF12):c.898G>A(p.Gly300Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 1,612,244 control chromosomes in the GnomAD database, including 3,004 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_207037.2 missense
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 |
---|---|---|---|---|---|---|---|
TCF12 | NM_207037.2 | c.898G>A | p.Gly300Ser | missense_variant | 11/21 | ENST00000333725.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF12 | ENST00000333725.10 | c.898G>A | p.Gly300Ser | missense_variant | 11/21 | 1 | NM_207037.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0401 AC: 6086AN: 151674Hom.: 370 Cov.: 31
GnomAD3 exomes AF: 0.0628 AC: 15703AN: 250048Hom.: 1570 AF XY: 0.0538 AC XY: 7283AN XY: 135270
GnomAD4 exome AF: 0.0391 AC: 57090AN: 1460460Hom.: 2630 Cov.: 32 AF XY: 0.0377 AC XY: 27376AN XY: 726568
GnomAD4 genome ? AF: 0.0402 AC: 6104AN: 151784Hom.: 374 Cov.: 31 AF XY: 0.0417 AC XY: 3094AN XY: 74188
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 25, 2018 | This variant is associated with the following publications: (PMID: 26264438) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at