rs150750750
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_022095.4(ZNF335):c.3820-7_3820-6del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000597 in 1,613,774 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0030 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00034 ( 2 hom. )
Consequence
ZNF335
NM_022095.4 splice_region, splice_polypyrimidine_tract, intron
NM_022095.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.506
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 20-45949256-AGG-A is Benign according to our data. Variant chr20-45949256-AGG-A is described in ClinVar as [Likely_benign]. Clinvar id is 437354.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00303 (461/152202) while in subpopulation AFR AF= 0.0102 (422/41524). AF 95% confidence interval is 0.00936. There are 1 homozygotes in gnomad4. There are 234 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF335 | NM_022095.4 | c.3820-7_3820-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000322927.3 | |||
ZNF335 | XM_005260504.5 | c.3817-7_3817-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
ZNF335 | XM_047440363.1 | c.3820-7_3820-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF335 | ENST00000322927.3 | c.3820-7_3820-6del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_022095.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00302 AC: 460AN: 152084Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000849 AC: 213AN: 250912Hom.: 1 AF XY: 0.000707 AC XY: 96AN XY: 135744
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GnomAD4 exome AF: 0.000343 AC: 502AN: 1461572Hom.: 2 AF XY: 0.000300 AC XY: 218AN XY: 727090
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GnomAD4 genome ? AF: 0.00303 AC: 461AN: 152202Hom.: 1 Cov.: 32 AF XY: 0.00314 AC XY: 234AN XY: 74420
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 23, 2015 | - - |
Microcephalic primordial dwarfism due to ZNF335 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 18, 2023 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -30
Find out detailed SpliceAI scores and Pangolin per-transcript scores at