chr18-74634993-C-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_017757.3(ZNF407):āc.3974C>Gā(p.Pro1325Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,848 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_017757.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF407 | NM_017757.3 | c.3974C>G | p.Pro1325Arg | missense_variant | 2/9 | ENST00000299687.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF407 | ENST00000299687.10 | c.3974C>G | p.Pro1325Arg | missense_variant | 2/9 | 1 | NM_017757.3 | P2 | |
ZNF407 | ENST00000577538.5 | c.3974C>G | p.Pro1325Arg | missense_variant | 1/7 | 2 | A2 | ||
ZNF407 | ENST00000309902.10 | c.3974C>G | p.Pro1325Arg | missense_variant | 1/4 | 2 | |||
ZNF407 | ENST00000582337.5 | c.3974C>G | p.Pro1325Arg | missense_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249038Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135162
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461680Hom.: 0 Cov.: 41 AF XY: 0.00 AC XY: 0AN XY: 727122
GnomAD4 genome AF: 0.000138 AC: 21AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74334
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 01, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at