16-72788110-TGCTGCTGCTGCTGCTGTAGTTGCC-TGCTGCTGCTGCTGCTGTAGTTGCCGCTGCTGCTGCTGCTGTAGTTGCC
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_006885.4(ZFHX3):c.10142_10165dupGGCAACTACAGCAGCAGCAGCAGC(p.Arg3381_Gln3388dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 1,599,246 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 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
ZFHX3
NM_006885.4 conservative_inframe_insertion
NM_006885.4 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.680
Genes affected
ZFHX3 (HGNC:777): (zinc finger homeobox 3) This gene encodes a transcription factor with multiple homeodomains and zinc finger motifs, and regulates myogenic and neuronal differentiation. The encoded protein suppresses expression of the alpha-fetoprotein gene by binding to an AT-rich enhancer motif. The protein has also been shown to negatively regulate c-Myb, and transactivate the cell cycle inhibitor cyclin-dependent kinase inhibitor 1A (also known as p21CIP1). This gene is reported to function as a tumor suppressor in several cancers, and sequence variants of this gene are also associated with atrial fibrillation. Multiple transcript variants expressed from alternate promoters and encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 18 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151352Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000125 AC: 3AN: 240058Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 130176
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GnomAD4 exome AF: 0.0000124 AC: 18AN: 1447894Hom.: 0 Cov.: 34 AF XY: 0.0000125 AC XY: 9AN XY: 719730
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GnomAD4 genome AF: 0.0000198 AC: 3AN: 151352Hom.: 0 Cov.: 32 AF XY: 0.0000406 AC XY: 3AN XY: 73952
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Not reported inComputational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at