NM_001379286.1:c.3467C>T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001379286.1(ZNF423):c.3467C>T(p.Pro1156Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000066 in 1,604,970 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001379286.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF423 | NM_001379286.1 | c.3467C>T | p.Pro1156Leu | missense_variant | Exon 4 of 8 | ENST00000563137.7 | NP_001366215.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF423 | ENST00000563137.7 | c.3467C>T | p.Pro1156Leu | missense_variant | Exon 4 of 8 | 5 | NM_001379286.1 | ENSP00000455588.3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152124Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000133 AC: 32AN: 240812Hom.: 1 AF XY: 0.000145 AC XY: 19AN XY: 130708
GnomAD4 exome AF: 0.0000702 AC: 102AN: 1452728Hom.: 3 Cov.: 31 AF XY: 0.0000664 AC XY: 48AN XY: 722802
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3443C>T (p.P1148L) alteration is located in exon 5 (coding exon 4) of the ZNF423 gene. This alteration results from a C to T substitution at nucleotide position 3443, causing the proline (P) at amino acid position 1148 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
The P1148L variant in the ZNF423 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The P1148L variant is observed in 14/11518 (0.12%) alleles from individuals of Latino background, in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The P1148L variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved in mammals. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret P1148L as a variant of uncertain significance. -
Nephronophthisis 14 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at