rs117132825
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_022095.4(ZNF335):c.1963C>T(p.Pro655Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.012 in 1,614,152 control chromosomes in the GnomAD database, including 259 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_022095.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF335 | NM_022095.4 | c.1963C>T | p.Pro655Ser | missense_variant | 14/28 | ENST00000322927.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF335 | ENST00000322927.3 | c.1963C>T | p.Pro655Ser | missense_variant | 14/28 | 1 | NM_022095.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00763 AC: 1161AN: 152164Hom.: 16 Cov.: 32
GnomAD3 exomes AF: 0.0117 AC: 2944AN: 251418Hom.: 58 AF XY: 0.0139 AC XY: 1886AN XY: 135894
GnomAD4 exome AF: 0.0124 AC: 18177AN: 1461870Hom.: 243 Cov.: 33 AF XY: 0.0136 AC XY: 9875AN XY: 727238
GnomAD4 genome AF: 0.00760 AC: 1158AN: 152282Hom.: 16 Cov.: 32 AF XY: 0.00783 AC XY: 583AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 27, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 25, 2023 | See Variant Classification Assertion Criteria. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 24, 2014 | - - |
ZNF335-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 05, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at