chr16-88427506-C-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001367624.2(ZNF469):c.36C>A(p.Pro12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000979 in 1,531,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P12P) has been classified as Likely benign.
Frequency
Consequence
NM_001367624.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF469 | NM_001367624.2 | c.36C>A | p.Pro12= | synonymous_variant | 3/3 | ENST00000565624.3 | |
LOC112268182 | XR_007065178.1 | n.251-1240G>T | intron_variant, non_coding_transcript_variant | ||||
ZNF469 | XM_047434810.1 | c.36C>A | p.Pro12= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF469 | ENST00000565624.3 | c.36C>A | p.Pro12= | synonymous_variant | 3/3 | NM_001367624.2 | A2 | ||
ZNF469 | ENST00000437464.1 | c.36C>A | p.Pro12= | synonymous_variant | 1/2 | 5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000384 AC: 5AN: 130234Hom.: 0 AF XY: 0.0000282 AC XY: 2AN XY: 71012
GnomAD4 exome AF: 0.00000870 AC: 12AN: 1379204Hom.: 0 Cov.: 32 AF XY: 0.00000735 AC XY: 5AN XY: 680020
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152274Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | ZNF469: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at