19-44428529-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014518.4(ZNF229):c.2252A>G(p.Gln751Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000583 in 1,613,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 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. Q751P) 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>G | p.Gln751Arg | missense_variant | 6/6 | ENST00000614049.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF229 | ENST00000614049.5 | c.2252A>G | p.Gln751Arg | missense_variant | 6/6 | 1 | NM_014518.4 | A2 | |
ZNF229 | ENST00000613197.4 | c.2234A>G | p.Gln745Arg | missense_variant | 6/6 | 1 | P4 | ||
ZNF229 | ENST00000620012.4 | c.*2455A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 1 | ||||
ZNF229 | ENST00000591289.5 | n.523-10983A>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000659 AC: 10AN: 151790Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000519 AC: 13AN: 250704Hom.: 0 AF XY: 0.0000885 AC XY: 12AN XY: 135668
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461864Hom.: 0 Cov.: 30 AF XY: 0.0000688 AC XY: 50AN XY: 727236
GnomAD4 genome ? AF: 0.0000659 AC: 10AN: 151790Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5AN XY: 74148
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.2252A>G (p.Q751R) alteration is located in exon 6 (coding exon 4) of the ZNF229 gene. This alteration results from a A to G substitution at nucleotide position 2252, causing the glutamine (Q) at amino acid position 751 to be replaced by an arginine (R). 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