rs527665020
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_207037.2(TCF12):c.75+58_75+65delGTTTGTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000248 in 1,605,812 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
TCF12
NM_207037.2 intron
NM_207037.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.54
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 -8 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00118 (180/151940) while in subpopulation AFR AF= 0.00417 (173/41446). AF 95% confidence interval is 0.00367. There are 0 homozygotes in gnomad4. There are 87 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High AC in GnomAd4 at 180 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TCF12 | NM_207037.2 | c.75+58_75+65delGTTTGTTT | intron_variant | Intron 2 of 20 | ENST00000333725.10 | NP_996920.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00118 AC: 179AN: 151822Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.000324 AC: 80AN: 246558Hom.: 0 AF XY: 0.000233 AC XY: 31AN XY: 133210
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GnomAD4 exome AF: 0.000151 AC: 219AN: 1453872Hom.: 0 AF XY: 0.000142 AC XY: 103AN XY: 723710
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GnomAD4 genome AF: 0.00118 AC: 180AN: 151940Hom.: 0 Cov.: 30 AF XY: 0.00117 AC XY: 87AN XY: 74252
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Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at