17-49317640-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145365.3(ZNF652):c.86G>A(p.Arg29His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,850 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R29C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001145365.3 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 |
---|---|---|---|---|---|---|---|
ZNF652 | NM_001145365.3 | c.86G>A | p.Arg29His | missense_variant | 2/6 | ENST00000430262.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF652 | ENST00000430262.3 | c.86G>A | p.Arg29His | missense_variant | 2/6 | 1 | NM_001145365.3 | P1 | |
ZNF652 | ENST00000362063.6 | c.86G>A | p.Arg29His | missense_variant | 2/6 | 1 | P1 | ||
FLJ40194 | ENST00000655089.1 | n.913C>T | non_coding_transcript_exon_variant | 5/6 | |||||
ZNF652 | ENST00000508237.5 | c.86G>A | p.Arg29His | missense_variant, NMD_transcript_variant | 3/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251208Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135780
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461542Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727014
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2023 | The c.86G>A (p.R29H) alteration is located in exon 2 (coding exon 1) of the ZNF652 gene. This alteration results from a G to A substitution at nucleotide position 86, causing the arginine (R) at amino acid position 29 to be replaced by a histidine (H). 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