chr20-45967900-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_022095.4(ZNF335):c.648G>A(p.Pro216=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,612,596 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00010 ( 4 hom. )
Consequence
ZNF335
NM_022095.4 synonymous
NM_022095.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.91
Genes affected
ZNF335 (HGNC:15807): (zinc finger protein 335) The protein encoded by this gene enhances transcriptional activation by ligand-bound nuclear hormone receptors. However, it does this not by direct interaction with the receptor, but by direct interaction with the nuclear hormone receptor transcriptional coactivator NRC. The encoded protein may function by altering local chromatin structure. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 20-45967900-C-T is Benign according to our data. Variant chr20-45967900-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 212654.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
BP7
Synonymous conserved (PhyloP=-3.91 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF335 | NM_022095.4 | c.648G>A | p.Pro216= | synonymous_variant | 5/28 | ENST00000322927.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF335 | ENST00000322927.3 | c.648G>A | p.Pro216= | synonymous_variant | 5/28 | 1 | NM_022095.4 | P1 | |
ZNF335 | ENST00000476822.1 | n.981G>A | non_coding_transcript_exon_variant | 3/5 | 2 | ||||
ZNF335 | ENST00000494955.1 | n.959G>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152194Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000201 AC: 50AN: 248646Hom.: 1 AF XY: 0.000155 AC XY: 21AN XY: 135098
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GnomAD4 exome AF: 0.000101 AC: 147AN: 1460284Hom.: 4 Cov.: 73 AF XY: 0.0000936 AC XY: 68AN XY: 726478
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GnomAD4 genome AF: 0.000164 AC: 25AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74478
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 27, 2014 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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