chr18-14105845-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145287.4(ZNF519):c.695T>C(p.Ile232Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000228 in 1,603,514 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145287.4 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 |
---|---|---|---|---|---|---|---|
ZNF519 | NM_145287.4 | c.695T>C | p.Ile232Thr | missense_variant | 3/3 | ENST00000590202.3 | |
ZNF519 | NR_033354.2 | n.162-20769T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF519 | ENST00000590202.3 | c.695T>C | p.Ile232Thr | missense_variant | 3/3 | 1 | NM_145287.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000276 AC: 42AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000195 AC: 47AN: 240698Hom.: 0 AF XY: 0.000191 AC XY: 25AN XY: 130592
GnomAD4 exome AF: 0.000221 AC: 321AN: 1451212Hom.: 0 Cov.: 34 AF XY: 0.000222 AC XY: 160AN XY: 721578
GnomAD4 genome ? AF: 0.000295 AC: 45AN: 152302Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2022 | The c.695T>C (p.I232T) alteration is located in exon 3 (coding exon 3) of the ZNF519 gene. This alteration results from a T to C substitution at nucleotide position 695, causing the isoleucine (I) at amino acid position 232 to be replaced by a threonine (T). 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