chr14-102319941-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018335.6(ZNF839):c.176C>A(p.Pro59His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000091 in 1,197,716 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 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. P59R) has been classified as Uncertain significance.
Frequency
Consequence
NM_018335.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF839 | NM_018335.6 | c.176C>A | p.Pro59His | missense_variant | 1/8 | ENST00000442396.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF839 | ENST00000442396.7 | c.176C>A | p.Pro59His | missense_variant | 1/8 | 5 | NM_018335.6 | A2 | |
ZNF839 | ENST00000558850.5 | c.-61+2275C>A | intron_variant | 2 | P2 | ||||
ZNF839 | ENST00000559185.5 | c.-61+423C>A | intron_variant | 2 | P2 | ||||
ZNF839 | ENST00000559098.5 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000669 AC: 10AN: 149446Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000944 AC: 99AN: 1048270Hom.: 0 Cov.: 30 AF XY: 0.0000810 AC XY: 41AN XY: 506068
GnomAD4 genome AF: 0.0000669 AC: 10AN: 149446Hom.: 0 Cov.: 32 AF XY: 0.0000549 AC XY: 4AN XY: 72868
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 09, 2022 | The c.176C>A (p.P59H) alteration is located in exon 1 (coding exon 1) of the ZNF839 gene. This alteration results from a C to A substitution at nucleotide position 176, causing the proline (P) at amino acid position 59 to be replaced by a histidine (H). 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