13-99970413-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGC
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_033132.5(ZIC5):c.1161_1190delGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC(p.Pro388_Pro397del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 984,586 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.000013 ( 1 hom. )
Consequence
ZIC5
NM_033132.5 disruptive_inframe_deletion
NM_033132.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.56
Genes affected
ZIC5 (HGNC:20322): (Zic family member 5) This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. The encoded protein may act as a transcriptional repressor. Studies in mouse and Xenopus support a role for this gene in neural crest development. Elevated expression of this gene has been observed in various human cancers and may contribute to cancer progression. This gene is closely linked to a related family member on chromosome 13. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_033132.5
BS2
High AC in GnomAdExome4 at 13 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZIC5 | NM_033132.5 | c.1161_1190delGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC | p.Pro388_Pro397del | disruptive_inframe_deletion | 1/2 | ENST00000267294.5 | NP_149123.3 | |
ZIC5 | NR_146224.1 | n.1467_1496delGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD3 genomes
Cov.:
0
GnomAD4 exome AF: 0.0000132 AC: 13AN: 984586Hom.: 1 AF XY: 0.0000169 AC XY: 8AN XY: 472584
GnomAD4 exome
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8
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GnomAD4 genome Cov.: 0
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0
ClinVar
Not reported inComputational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at