rs587780522
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_017757.3(ZNF407):c.1258A>G(p.Ile420Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,820 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 Likely benign (★).
Frequency
Consequence
NM_017757.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF407 | NM_017757.3 | c.1258A>G | p.Ile420Val | missense_variant | 2/9 | ENST00000299687.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF407 | ENST00000299687.10 | c.1258A>G | p.Ile420Val | missense_variant | 2/9 | 1 | NM_017757.3 | P2 | |
ZNF407 | ENST00000577538.5 | c.1258A>G | p.Ile420Val | missense_variant | 1/7 | 2 | A2 | ||
ZNF407 | ENST00000309902.10 | c.1258A>G | p.Ile420Val | missense_variant | 1/4 | 2 | |||
ZNF407 | ENST00000582337.5 | c.1258A>G | p.Ile420Val | missense_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248898Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135156
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461614Hom.: 0 Cov.: 53 AF XY: 0.0000110 AC XY: 8AN XY: 727080
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 02, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at