rs777049090
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017757.3(ZNF407):c.5863G>A(p.Glu1955Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000169 in 1,417,370 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_017757.3 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 |
---|---|---|---|---|---|---|---|
ZNF407 | NM_017757.3 | c.5863G>A | p.Glu1955Lys | missense_variant | 9/9 | ENST00000299687.10 | |
ZNF407 | NM_001384475.1 | c.5863G>A | p.Glu1955Lys | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF407 | ENST00000299687.10 | c.5863G>A | p.Glu1955Lys | missense_variant | 9/9 | 1 | NM_017757.3 | P2 | |
ZNF407 | ENST00000579200.1 | n.2303G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.0000169 AC: 24AN: 1417370Hom.: 0 Cov.: 29 AF XY: 0.0000114 AC XY: 8AN XY: 701238
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 03, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.5863G>A (p.E1955K) alteration is located in exon 8 (coding exon 8) of the ZNF407 gene. This alteration results from a G to A substitution at nucleotide position 5863, causing the glutamic acid (E) at amino acid position 1955 to be replaced by a lysine (K). 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