1-247100402-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001142572.2(ZNF669):āc.1109T>Cā(p.Leu370Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,611,556 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001142572.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF669 | NM_001142572.2 | c.1109T>C | p.Leu370Ser | missense_variant | 4/4 | ENST00000448299.7 | NP_001136044.1 | |
ZNF669 | NM_024804.3 | c.1367T>C | p.Leu456Ser | missense_variant | 4/4 | NP_079080.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF669 | ENST00000448299.7 | c.1109T>C | p.Leu370Ser | missense_variant | 4/4 | 1 | NM_001142572.2 | ENSP00000404370 | A2 | |
ZNF669 | ENST00000343381.10 | c.1367T>C | p.Leu456Ser | missense_variant | 4/4 | 1 | ENSP00000342818 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000484 AC: 12AN: 247722Hom.: 0 AF XY: 0.0000597 AC XY: 8AN XY: 134114
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1459328Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 726060
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2023 | The c.1367T>C (p.L456S) alteration is located in exon 4 (coding exon 4) of the ZNF669 gene. This alteration results from a T to C substitution at nucleotide position 1367, causing the leucine (L) at amino acid position 456 to be replaced by a serine (S). 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