chr9-106924377-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_ModerateBP7BS1BS2_Supporting
The NM_021224.6(ZNF462):c.465C>T(p.His155=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000799 in 1,613,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000083 ( 0 hom. )
Consequence
ZNF462
NM_021224.6 synonymous
NM_021224.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.403
Genes affected
ZNF462 (HGNC:21684): (zinc finger protein 462) The protein encoded by this gene belongs to C2H2-type zinc finger family of proteins. It contains multiple C2H2-type zinc fingers and may be involved in transcriptional regulation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 9-106924377-C-T is Benign according to our data. Variant chr9-106924377-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3044979.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.403 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0000828 (121/1461874) while in subpopulation NFE AF= 0.0000998 (111/1112006). AF 95% confidence interval is 0.0000839. There are 0 homozygotes in gnomad4_exome. There are 50 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 8 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF462 | NM_021224.6 | c.465C>T | p.His155= | synonymous_variant | 3/13 | ENST00000277225.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF462 | ENST00000277225.10 | c.465C>T | p.His155= | synonymous_variant | 3/13 | 1 | NM_021224.6 | P1 | |
ZNF462 | ENST00000472574.1 | c.280+185C>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152098Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000398 AC: 10AN: 250964Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135788
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GnomAD4 exome AF: 0.0000828 AC: 121AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.0000688 AC XY: 50AN XY: 727240
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74290
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ZNF462-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 06, 2019 | This variant is classified as likely 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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Name
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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