16-30583059-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152458.7(ZNF785):c.719G>A(p.Arg240Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,607,950 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 (★).
Frequency
Consequence
NM_152458.7 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 |
---|---|---|---|---|---|---|---|
ZNF785 | NM_152458.7 | c.719G>A | p.Arg240Lys | missense_variant | 3/3 | ENST00000395216.3 | |
ZNF785 | XM_011545753.3 | c.758G>A | p.Arg253Lys | missense_variant | 3/4 | ||
ZNF785 | XM_017022967.3 | c.719G>A | p.Arg240Lys | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF785 | ENST00000395216.3 | c.719G>A | p.Arg240Lys | missense_variant | 3/3 | 1 | NM_152458.7 | P2 | |
ENST00000492040.1 | n.687C>T | non_coding_transcript_exon_variant | 2/2 | 1 | |||||
ZNF785 | ENST00000470110.2 | c.674G>A | p.Arg225Lys | missense_variant | 3/4 | 2 | A2 | ||
ENST00000657071.1 | n.903C>T | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes AF: 0.0000274 AC: 4AN: 146192Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461758Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727198
GnomAD4 genome AF: 0.0000274 AC: 4AN: 146192Hom.: 0 Cov.: 32 AF XY: 0.0000421 AC XY: 3AN XY: 71268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 22, 2023 | The c.719G>A (p.R240K) alteration is located in exon 3 (coding exon 3) of the ZNF785 gene. This alteration results from a G to A substitution at nucleotide position 719, causing the arginine (R) at amino acid position 240 to be replaced by a lysine (K). 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