19-44428529-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014518.4(ZNF229):c.2252A>C(p.Gln751Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,772 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q751R) has been classified as Uncertain significance.
Frequency
Consequence
NM_014518.4 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 |
---|---|---|---|---|---|---|---|
ZNF229 | NM_014518.4 | c.2252A>C | p.Gln751Pro | missense_variant | 6/6 | ENST00000614049.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF229 | ENST00000614049.5 | c.2252A>C | p.Gln751Pro | missense_variant | 6/6 | 1 | NM_014518.4 | A2 | |
ZNF229 | ENST00000613197.4 | c.2234A>C | p.Gln745Pro | missense_variant | 6/6 | 1 | P4 | ||
ZNF229 | ENST00000620012.4 | c.*2455A>C | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 1 | ||||
ZNF229 | ENST00000591289.5 | n.523-10983A>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 151790Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250704Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135668
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461864Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 727236
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 151908Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.2252A>C (p.Q751P) alteration is located in exon 6 (coding exon 4) of the ZNF229 gene. This alteration results from a A to C substitution at nucleotide position 2252, causing the glutamine (Q) at amino acid position 751 to be replaced by a proline (P). 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