19-56539058-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020828.2(ZFP28):c.40C>A(p.Pro14Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 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. P14Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_020828.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZFP28 | NM_020828.2 | c.40C>A | p.Pro14Thr | missense_variant | Exon 1 of 8 | ENST00000301318.8 | NP_065879.1 | |
ZFP28 | NM_001308440.2 | c.40C>A | p.Pro14Thr | missense_variant | Exon 1 of 7 | NP_001295369.1 | ||
ZFP28 | XM_011526463.4 | c.182-567C>A | intron_variant | Intron 1 of 7 | XP_011524765.2 | |||
ZFP28 | XM_011526462.4 | c.-546C>A | upstream_gene_variant | XP_011524764.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZFP28 | ENST00000301318.8 | c.40C>A | p.Pro14Thr | missense_variant | Exon 1 of 8 | 1 | NM_020828.2 | ENSP00000301318.3 | ||
ZFP28 | ENST00000591844.5 | c.40C>A | p.Pro14Thr | missense_variant | Exon 1 of 7 | 1 | ENSP00000468603.1 | |||
ZFP28 | ENST00000589836.1 | n.-72C>A | upstream_gene_variant | 5 | ENSP00000465853.1 | |||||
ZFP28 | ENST00000594386.1 | n.-11C>A | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.40C>A (p.P14T) alteration is located in exon 1 (coding exon 1) of the ZFP28 gene. This alteration results from a C to A substitution at nucleotide position 40, causing the proline (P) at amino acid position 14 to be replaced by a threonine (T). 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