rs10047994
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_207037.2(TCF12):āc.1894T>Cā(p.Leu632=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00616 in 1,614,150 control chromosomes in the GnomAD database, including 538 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.032 ( 272 hom., cov: 32)
Exomes š: 0.0035 ( 266 hom. )
Consequence
TCF12
NM_207037.2 synonymous
NM_207037.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.14
Genes affected
TCF12 (HGNC:11623): (transcription factor 12) The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 15-57273178-T-C is Benign according to our data. Variant chr15-57273178-T-C is described in ClinVar as [Benign]. Clinvar id is 263278.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-57273178-T-C is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCF12 | NM_207037.2 | c.1894T>C | p.Leu632= | synonymous_variant | 19/21 | ENST00000333725.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF12 | ENST00000333725.10 | c.1894T>C | p.Leu632= | synonymous_variant | 19/21 | 1 | NM_207037.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0320 AC: 4876AN: 152152Hom.: 272 Cov.: 32
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GnomAD3 exomes AF: 0.00845 AC: 2124AN: 251402Hom.: 90 AF XY: 0.00619 AC XY: 841AN XY: 135870
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GnomAD4 exome AF: 0.00346 AC: 5056AN: 1461880Hom.: 266 Cov.: 31 AF XY: 0.00294 AC XY: 2138AN XY: 727240
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GnomAD4 genome ? AF: 0.0321 AC: 4887AN: 152270Hom.: 272 Cov.: 32 AF XY: 0.0311 AC XY: 2315AN XY: 74448
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 31, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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