chr2-218638535-CA-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_001379659.1(ZNF142):c.5467del(p.Cys1823AlafsTer90) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,860 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
ZNF142
NM_001379659.1 frameshift
NM_001379659.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.31
Genes affected
ZNF142 (HGNC:12927): (zinc finger protein 142) The protein encoded by this gene belongs to the Kruppel family of C2H2-type zinc finger proteins. It contains 31 C2H2-type zinc fingers and may be involved in transcriptional regulation. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0348 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF142 | NM_001379659.1 | c.5467del | p.Cys1823AlafsTer90 | frameshift_variant | 11/11 | ENST00000411696.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF142 | ENST00000411696.7 | c.5467del | p.Cys1823AlafsTer90 | frameshift_variant | 11/11 | 5 | NM_001379659.1 | P1 | |
ZNF142 | ENST00000449707.5 | c.4867del | p.Cys1623AlafsTer90 | frameshift_variant | 10/10 | 1 | |||
ZNF142 | ENST00000450765.5 | c.*4692del | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 1 | ||||
ZNF142 | ENST00000433921.5 | c.*4692del | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247614Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134266
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GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457860Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 724522
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 01, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge; Frameshift variant predicted to result in protein truncation, as the last 65 amino acids are replaced with 89 different amino acids - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at