19-11867791-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001348719.2(ZNF439):c.737C>T(p.Pro246Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,614,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001348719.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF439 | NM_001348719.2 | c.737C>T | p.Pro246Leu | missense_variant | Exon 4 of 4 | ENST00000682736.1 | NP_001335648.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF439 | ENST00000682736.1 | c.737C>T | p.Pro246Leu | missense_variant | Exon 4 of 4 | NM_001348719.2 | ENSP00000506930.1 | |||
ZNF439 | ENST00000304030.2 | c.722C>T | p.Pro241Leu | missense_variant | Exon 3 of 3 | 1 | ENSP00000305077.2 | |||
ZNF439 | ENST00000455282.1 | c.314C>T | p.Pro105Leu | missense_variant | Exon 3 of 3 | 1 | ENSP00000395632.1 | |||
ZNF439 | ENST00000592534.1 | n.120-15760C>T | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251244Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135796
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461796Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727202
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.722C>T (p.P241L) alteration is located in exon 3 (coding exon 3) of the ZNF439 gene. This alteration results from a C to T substitution at nucleotide position 722, causing the proline (P) at amino acid position 241 to be replaced by a leucine (L). 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