chr19-21537024-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001415.4(ZNF429):c.971G>A(p.Arg324Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,608,052 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_001001415.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF429 | NM_001001415.4 | c.971G>A | p.Arg324Gln | missense_variant | 4/4 | ENST00000358491.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF429 | ENST00000358491.9 | c.971G>A | p.Arg324Gln | missense_variant | 4/4 | 3 | NM_001001415.4 | P1 | |
ZNF429 | ENST00000597078.5 | c.227-4740G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000887 AC: 13AN: 146552Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000323 AC: 8AN: 247842Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134790
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461372Hom.: 0 Cov.: 36 AF XY: 0.0000165 AC XY: 12AN XY: 726988
GnomAD4 genome AF: 0.0000886 AC: 13AN: 146680Hom.: 0 Cov.: 33 AF XY: 0.000112 AC XY: 8AN XY: 71494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.971G>A (p.R324Q) alteration is located in exon 4 (coding exon 4) of the ZNF429 gene. This alteration results from a G to A substitution at nucleotide position 971, causing the arginine (R) at amino acid position 324 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