9-101408158-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003452.4(ZNF189):c.390C>G(p.Phe130Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003452.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF189 | ENST00000339664.7 | c.390C>G | p.Phe130Leu | missense_variant | Exon 3 of 3 | 1 | NM_003452.4 | ENSP00000342019.2 | ||
ZNF189 | ENST00000374861.7 | c.348C>G | p.Phe116Leu | missense_variant | Exon 3 of 3 | 1 | ENSP00000363995.3 | |||
ZNF189 | ENST00000259395.4 | c.264C>G | p.Phe88Leu | missense_variant | Exon 4 of 4 | 1 | ENSP00000259395.4 | |||
ZNF189 | ENST00000615466.1 | c.*211C>G | 3_prime_UTR_variant | Exon 4 of 4 | 3 | ENSP00000483461.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.390C>G (p.F130L) alteration is located in exon 3 (coding exon 3) of the ZNF189 gene. This alteration results from a C to G substitution at nucleotide position 390, causing the phenylalanine (F) at amino acid position 130 to be replaced by a leucine (L). 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