19-9566008-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001008727.5(ZNF121):āc.1105A>Gā(p.Ile369Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000593 in 151,806 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 (ā ).
Frequency
Consequence
NM_001008727.5 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 |
---|---|---|---|---|---|---|---|
ZNF121 | NM_001008727.5 | c.1105A>G | p.Ile369Val | missense_variant | 4/4 | ENST00000320451.7 | |
ZNF121 | NM_001308269.3 | c.1105A>G | p.Ile369Val | missense_variant | 5/5 | ||
ZNF121 | XM_017027239.2 | c.1105A>G | p.Ile369Val | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF121 | ENST00000320451.7 | c.1105A>G | p.Ile369Val | missense_variant | 4/4 | 3 | NM_001008727.5 | P1 | |
ZNF121 | ENST00000586602.5 | c.1105A>G | p.Ile369Val | missense_variant | 6/6 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000593 AC: 9AN: 151686Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249890Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135094
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000226 AC: 33AN: 1458118Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 725332
GnomAD4 genome AF: 0.0000593 AC: 9AN: 151806Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74246
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2022 | The c.1105A>G (p.I369V) alteration is located in exon 4 (coding exon 2) of the ZNF121 gene. This alteration results from a A to G substitution at nucleotide position 1105, causing the isoleucine (I) at amino acid position 369 to be replaced by a valine (V). 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