chr7-149848145-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001099220.3(ZNF862):c.652C>T(p.Arg218Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,614,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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. R218Q) has been classified as Likely benign.
Frequency
Consequence
NM_001099220.3 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 | UniProt |
---|---|---|---|---|---|---|---|
ZNF862 | NM_001099220.3 | c.652C>T | p.Arg218Trp | missense_variant | 4/8 | ENST00000223210.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF862 | ENST00000223210.5 | c.652C>T | p.Arg218Trp | missense_variant | 4/8 | 5 | NM_001099220.3 | P1 | |
ZNF862 | ENST00000488265.1 | n.19C>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249184Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135184
GnomAD4 exome AF: 0.0000643 AC: 94AN: 1461708Hom.: 0 Cov.: 32 AF XY: 0.0000536 AC XY: 39AN XY: 727136
GnomAD4 genome ? AF: 0.0000656 AC: 10AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.652C>T (p.R218W) alteration is located in exon 4 (coding exon 4) of the ZNF862 gene. This alteration results from a C to T substitution at nucleotide position 652, causing the arginine (R) at amino acid position 218 to be replaced by a tryptophan (W). 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