chr14-88607345-ACCCCATCTCACCCTGCAAGTGAGTACCATCCCCCCATCTCACCCTGCAAGTGAGTACCATCC-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_024824.5(ZC3H14):c.1868+3_1868+64del variant causes a splice donor, splice donor 5th base, coding sequence, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,610,838 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 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
ZC3H14
NM_024824.5 splice_donor, splice_donor_5th_base, coding_sequence, intron
NM_024824.5 splice_donor, splice_donor_5th_base, coding_sequence, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.57
Genes affected
ZC3H14 (HGNC:20509): (zinc finger CCCH-type containing 14) The protein encoded by this gene is a poly(A)-binding protein that can affect gene expression and poly(A) tail length. The encoded protein may influence mRNA stability, nuclear export, and translation. [provided by RefSeq, May 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC3H14 | NM_024824.5 | c.1868+3_1868+64del | splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 13/17 | ENST00000251038.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H14 | ENST00000251038.10 | c.1868+3_1868+64del | splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 13/17 | 1 | NM_024824.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00000665 AC: 1AN: 150368Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460352Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 726468
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GnomAD4 genome AF: 0.00000665 AC: 1AN: 150486Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73532
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at