chr7-149847902-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.409C>T(p.Arg137Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 1,607,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R137Q) has been classified as Uncertain significance.
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.409C>T | p.Arg137Trp | missense_variant | 4/8 | ENST00000223210.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF862 | ENST00000223210.5 | c.409C>T | p.Arg137Trp | missense_variant | 4/8 | 5 | NM_001099220.3 | P1 | |
ZNF862 | ENST00000460379.1 | c.157C>T | p.Arg53Trp | missense_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000129 AC: 3AN: 233386Hom.: 0 AF XY: 0.0000158 AC XY: 2AN XY: 126598
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1454824Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 723060
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2023 | The c.409C>T (p.R137W) 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 409, causing the arginine (R) at amino acid position 137 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