chr19-47066434-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_015168.2(ZC3H4):c.3834C>T(p.Arg1278=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000767 in 1,571,922 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00045 ( 5 hom. )
Consequence
ZC3H4
NM_015168.2 synonymous
NM_015168.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.83
Genes affected
ZC3H4 (HGNC:17808): (zinc finger CCCH-type containing 4) This gene encodes a member of a family of CCCH (C-x8-C-x5-C-x3-H type) zinc finger domain-containing proteins. These zinc finger domains, which coordinate zinc finger binding and are characterized by three cysteine residues and one histidine residue, are nucleic acid-binding. Other family members are known to function in post-transcriptional regulation. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 19-47066434-G-A is Benign according to our data. Variant chr19-47066434-G-A is described in ClinVar as [Benign]. Clinvar id is 3053829.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.83 with no splicing effect.
BS2
?
High AC in GnomAd at 558 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC3H4 | NM_015168.2 | c.3834C>T | p.Arg1278= | synonymous_variant | 15/15 | ENST00000253048.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H4 | ENST00000253048.10 | c.3834C>T | p.Arg1278= | synonymous_variant | 15/15 | 1 | NM_015168.2 | P1 | |
ZC3H4 | ENST00000601973.1 | c.2655C>T | p.Arg885= | synonymous_variant | 8/8 | 5 | |||
ZC3H4 | ENST00000594019.5 | n.1684C>T | non_coding_transcript_exon_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00367 AC: 558AN: 152108Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00107 AC: 204AN: 191484Hom.: 1 AF XY: 0.000698 AC XY: 72AN XY: 103220
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GnomAD4 exome AF: 0.000452 AC: 642AN: 1419696Hom.: 5 Cov.: 31 AF XY: 0.000394 AC XY: 277AN XY: 702462
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GnomAD4 genome ? AF: 0.00371 AC: 564AN: 152226Hom.: 3 Cov.: 32 AF XY: 0.00359 AC XY: 267AN XY: 74430
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ZC3H4-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 07, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at