chr18-25225283-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_015461.3(ZNF521):c.2635G>A(p.Val879Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000052 in 1,614,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V879A) has been classified as Uncertain significance.
Frequency
Consequence
NM_015461.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF521 | NM_015461.3 | c.2635G>A | p.Val879Ile | missense_variant | 4/8 | ENST00000361524.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF521 | ENST00000361524.8 | c.2635G>A | p.Val879Ile | missense_variant | 4/8 | 1 | NM_015461.3 | P1 | |
ZNF521 | ENST00000584787.5 | c.1975G>A | p.Val659Ile | missense_variant | 3/7 | 1 | |||
ZNF521 | ENST00000399425.6 | c.2635G>A | p.Val879Ile | missense_variant, NMD_transcript_variant | 4/9 | 1 | |||
ZNF521 | ENST00000538137.6 | c.2635G>A | p.Val879Ile | missense_variant | 4/8 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251282Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135810
GnomAD4 exome AF: 0.0000506 AC: 74AN: 1461874Hom.: 0 Cov.: 32 AF XY: 0.0000578 AC XY: 42AN XY: 727236
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.2635G>A (p.V879I) alteration is located in exon 4 (coding exon 3) of the ZNF521 gene. This alteration results from a G to A substitution at nucleotide position 2635, causing the valine (V) at amino acid position 879 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at