19-20105283-G-C
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007138.2(ZNF90):c.193G>C(p.Val65Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,510 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.
Frequency
Consequence
NM_007138.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF90 | ENST00000418063.3 | c.193G>C | p.Val65Leu | missense_variant | Exon 3 of 4 | 1 | NM_007138.2 | ENSP00000410466.2 | ||
ZNF90 | ENST00000469078.5 | n.193G>C | non_coding_transcript_exon_variant | Exon 3 of 6 | 5 | ENSP00000420111.1 | ||||
ZNF90 | ENST00000473524.5 | n.193G>C | non_coding_transcript_exon_variant | Exon 3 of 5 | 3 | ENSP00000418166.1 | ||||
ZNF90 | ENST00000474284.1 | n.205G>C | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455510Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 724164 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at