rs200375993
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_015461.3(ZNF521):c.698C>T(p.Ser233Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000551 in 1,614,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_015461.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF521 | NM_015461.3 | c.698C>T | p.Ser233Phe | missense_variant | 4/8 | ENST00000361524.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF521 | ENST00000361524.8 | c.698C>T | p.Ser233Phe | missense_variant | 4/8 | 1 | NM_015461.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000355 AC: 54AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251300Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135808
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461870Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727236
GnomAD4 genome ? AF: 0.000355 AC: 54AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74418
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 17, 2023 | The c.698C>T (p.S233F) alteration is located in exon 4 (coding exon 3) of the ZNF521 gene. This alteration results from a C to T substitution at nucleotide position 698, causing the serine (S) at amino acid position 233 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing;provider interpretation | Geisinger Autism and Developmental Medicine Institute, Geisinger Health System | Feb 23, 2018 | This variant was identified in a 10 year old male with autism spectrum disorder, large stature, anxiety, compulsive behavior, and uncertain intellectual abilities. He is of Puerto Rican descent. The variant is present in the gnomAD Latino population at 0.0087% and as high as 1% in the Puerto Rican population from 1000Genomes. Computational prediction models are inconsistent. A second missense change in ZNF521 was also identified in trans. This is a gene of uncertain significance; no known human disorders have been clearly associated with this gene. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at