rs551678383
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_022095.4(ZNF335):c.815-3delC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,613,914 control chromosomes in the GnomAD database, including 119 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0069 ( 3 hom., cov: 32)
Exomes 𝑓: 0.011 ( 116 hom. )
Consequence
ZNF335
NM_022095.4 splice_region, intron
NM_022095.4 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.127
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 -16 ACMG points.
BP6
Variant 20-45967636-TG-T is Benign according to our data. Variant chr20-45967636-TG-T is described in ClinVar as [Benign]. Clinvar id is 130808.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00687 (1046/152280) while in subpopulation NFE AF= 0.0116 (789/68018). AF 95% confidence interval is 0.0109. There are 3 homozygotes in gnomad4. There are 463 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF335 | ENST00000322927.3 | c.815-3delC | splice_region_variant, intron_variant | Intron 5 of 27 | 1 | NM_022095.4 | ENSP00000325326.2 | |||
ZNF335 | ENST00000476822.1 | n.1148-3delC | splice_region_variant, intron_variant | Intron 3 of 4 | 2 | |||||
ZNF335 | ENST00000494955.1 | n.1126-3delC | splice_region_variant, intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00687 AC: 1046AN: 152162Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00684 AC: 1717AN: 251104Hom.: 9 AF XY: 0.00664 AC XY: 902AN XY: 135790
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GnomAD4 exome AF: 0.0113 AC: 16555AN: 1461634Hom.: 116 Cov.: 73 AF XY: 0.0108 AC XY: 7866AN XY: 727142
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GnomAD4 genome AF: 0.00687 AC: 1046AN: 152280Hom.: 3 Cov.: 32 AF XY: 0.00622 AC XY: 463AN XY: 74464
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Jan 14, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Sep 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
ZNF335: BP4, BS1, BS2 -
May 29, 2020
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
not specified Benign:1
Nov 19, 2015
Genetic Services Laboratory, University of Chicago
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Microcephalic primordial dwarfism due to ZNF335 deficiency Benign:1
Dec 05, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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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