19-12273042-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016264.4(ZNF44):c.1213C>T(p.Pro405Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,612,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016264.4 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 |
---|---|---|---|---|---|---|---|
ZNF44 | NM_016264.4 | c.1213C>T | p.Pro405Ser | missense_variant | 4/4 | ENST00000355684.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF44 | ENST00000355684.6 | c.1213C>T | p.Pro405Ser | missense_variant | 4/4 | 2 | NM_016264.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000185 AC: 28AN: 151038Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000239 AC: 60AN: 251148Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135842
GnomAD4 exome AF: 0.000114 AC: 167AN: 1461810Hom.: 0 Cov.: 35 AF XY: 0.000107 AC XY: 78AN XY: 727194
GnomAD4 genome AF: 0.000185 AC: 28AN: 151038Hom.: 0 Cov.: 32 AF XY: 0.000258 AC XY: 19AN XY: 73752
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.1357C>T (p.P453S) alteration is located in exon 5 (coding exon 5) of the ZNF44 gene. This alteration results from a C to T substitution at nucleotide position 1357, causing the proline (P) at amino acid position 453 to be replaced by a serine (S). 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