chr9-106924149-A-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.237A>T(p.Ser79=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000137 in 1,596,992 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 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
ZNF462
NM_021224.6 synonymous
NM_021224.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.537
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=-0.9).
BP6
Variant 9-106924149-A-T is Benign according to our data. Variant chr9-106924149-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 3046169.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.537 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0000657 (10/152128) while in subpopulation NFE AF= 0.000147 (10/68020). AF 95% confidence interval is 0.0000791. There are 0 homozygotes in gnomad4. There are 6 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 10 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.237A>T | p.Ser79= | synonymous_variant | 3/13 | ENST00000277225.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF462 | ENST00000277225.10 | c.237A>T | p.Ser79= | synonymous_variant | 3/13 | 1 | NM_021224.6 | P1 | |
ZNF462 | ENST00000472574.1 | c.237A>T | p.Ser79= | synonymous_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152128Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000597 AC: 14AN: 234378Hom.: 0 AF XY: 0.0000712 AC XY: 9AN XY: 126364
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GnomAD4 exome AF: 0.000145 AC: 209AN: 1444864Hom.: 0 Cov.: 31 AF XY: 0.000159 AC XY: 114AN XY: 717908
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74322
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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 | Oct 28, 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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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