15-56919557-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_207037.2(TCF12):c.-22-335G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00253 in 184,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0030 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00031 ( 0 hom. )
Consequence
TCF12
NM_207037.2 intron
NM_207037.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.491
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 15-56919557-G-A is Benign according to our data. Variant chr15-56919557-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1300946.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00301 (456/151730) while in subpopulation AFR AF= 0.0106 (441/41440). AF 95% confidence interval is 0.00982. There are 0 homozygotes in gnomad4. There are 207 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 450 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCF12 | NM_207037.2 | c.-22-335G>A | intron_variant | ENST00000333725.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF12 | ENST00000333725.10 | c.-22-335G>A | intron_variant | 1 | NM_207037.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00297 AC: 450AN: 151624Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.000308 AC: 10AN: 32486Hom.: 0 Cov.: 0 AF XY: 0.000382 AC XY: 6AN XY: 15712
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GnomAD4 genome ? AF: 0.00301 AC: 456AN: 151730Hom.: 0 Cov.: 31 AF XY: 0.00279 AC XY: 207AN XY: 74184
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 18, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at