chr19-47066875-C-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_015168.2(ZC3H4):c.3393G>C(p.Leu1131=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00253 in 1,598,566 control chromosomes in the GnomAD database, including 104 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 51 hom., cov: 33)
Exomes 𝑓: 0.0014 ( 53 hom. )
Consequence
ZC3H4
NM_015168.2 synonymous
NM_015168.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0200
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 19-47066875-C-G is Benign according to our data. Variant chr19-47066875-C-G is described in ClinVar as [Benign]. Clinvar id is 769023.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.02 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0136 (2065/152322) while in subpopulation AFR AF= 0.0469 (1952/41578). AF 95% confidence interval is 0.0452. There are 51 homozygotes in gnomad4. There are 962 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2063 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC3H4 | NM_015168.2 | c.3393G>C | p.Leu1131= | synonymous_variant | 15/15 | ENST00000253048.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H4 | ENST00000253048.10 | c.3393G>C | p.Leu1131= | synonymous_variant | 15/15 | 1 | NM_015168.2 | P1 | |
ZC3H4 | ENST00000601973.1 | c.2214G>C | p.Leu738= | synonymous_variant | 8/8 | 5 | |||
ZC3H4 | ENST00000594019.5 | n.1243G>C | non_coding_transcript_exon_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0136 AC: 2063AN: 152204Hom.: 52 Cov.: 33
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GnomAD3 exomes AF: 0.00335 AC: 758AN: 226384Hom.: 16 AF XY: 0.00269 AC XY: 337AN XY: 125318
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GnomAD4 exome AF: 0.00137 AC: 1975AN: 1446244Hom.: 53 Cov.: 33 AF XY: 0.00123 AC XY: 886AN XY: 719788
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GnomAD4 genome ? AF: 0.0136 AC: 2065AN: 152322Hom.: 51 Cov.: 33 AF XY: 0.0129 AC XY: 962AN XY: 74478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at