chr19-21183787-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_133473.4(ZNF431):c.1484G>A(p.Arg495Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000198 in 1,613,384 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_133473.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF431 | NM_133473.4 | c.1484G>A | p.Arg495Gln | missense_variant | 5/5 | ENST00000311048.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF431 | ENST00000311048.11 | c.1484G>A | p.Arg495Gln | missense_variant | 5/5 | 1 | NM_133473.4 | P1 | |
ZNF431 | ENST00000600692.5 | c.*1071G>A | 3_prime_UTR_variant | 6/6 | 5 | ||||
ZNF431 | ENST00000594425.5 | c.97-6078G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000527 AC: 8AN: 151780Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000562 AC: 14AN: 249180Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135064
GnomAD4 exome AF: 0.000213 AC: 311AN: 1461604Hom.: 0 Cov.: 31 AF XY: 0.000187 AC XY: 136AN XY: 727108
GnomAD4 genome ? AF: 0.0000527 AC: 8AN: 151780Hom.: 0 Cov.: 33 AF XY: 0.0000810 AC XY: 6AN XY: 74106
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.1484G>A (p.R495Q) alteration is located in exon 5 (coding exon 5) of the ZNF431 gene. This alteration results from a G to A substitution at nucleotide position 1484, causing the arginine (R) at amino acid position 495 to be replaced by a glutamine (Q). 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