rs759216909
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_022095.4(ZNF335):c.3444C>T(p.Thr1148=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000078 in 1,551,436 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000083 ( 0 hom. )
Consequence
ZNF335
NM_022095.4 synonymous
NM_022095.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.50
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 Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 20-45950262-G-A is Benign according to our data. Variant chr20-45950262-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 437344.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
BP7
?
Synonymous conserved (PhyloP=2.5 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF335 | NM_022095.4 | c.3444C>T | p.Thr1148= | synonymous_variant | 22/28 | ENST00000322927.3 | |
ZNF335 | XM_047440363.1 | c.3444C>T | p.Thr1148= | synonymous_variant | 21/27 | ||
ZNF335 | XM_005260504.5 | c.3441C>T | p.Thr1147= | synonymous_variant | 21/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF335 | ENST00000322927.3 | c.3444C>T | p.Thr1148= | synonymous_variant | 22/28 | 1 | NM_022095.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152108Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000498 AC: 10AN: 200710Hom.: 0 AF XY: 0.0000377 AC XY: 4AN XY: 106124
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GnomAD4 exome AF: 0.0000829 AC: 116AN: 1399328Hom.: 0 Cov.: 34 AF XY: 0.0000769 AC XY: 53AN XY: 689308
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GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152108Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74292
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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 | Feb 18, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 16, 2021 | - - |
Computational scores
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Name
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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