rs202084477
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017757.3(ZNF407):c.2493T>A(p.Asp831Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,613,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF407 | NM_017757.3 | c.2493T>A | p.Asp831Glu | missense_variant | 2/9 | ENST00000299687.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF407 | ENST00000299687.10 | c.2493T>A | p.Asp831Glu | missense_variant | 2/9 | 1 | NM_017757.3 | P2 | |
ZNF407 | ENST00000577538.5 | c.2493T>A | p.Asp831Glu | missense_variant | 1/7 | 2 | A2 | ||
ZNF407 | ENST00000309902.10 | c.2493T>A | p.Asp831Glu | missense_variant | 1/4 | 2 | |||
ZNF407 | ENST00000582337.5 | c.2493T>A | p.Asp831Glu | missense_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000562 AC: 14AN: 249172Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135176
GnomAD4 exome AF: 0.000105 AC: 154AN: 1461680Hom.: 0 Cov.: 42 AF XY: 0.000117 AC XY: 85AN XY: 727122
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152146Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.2493T>A (p.D831E) alteration is located in exon 1 (coding exon 1) of the ZNF407 gene. This alteration results from a T to A substitution at nucleotide position 2493, causing the aspartic acid (D) at amino acid position 831 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 07, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at