19-52155293-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001102657.3(ZNF836):c.2390G>A(p.Arg797Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000806 in 1,613,496 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 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. R797W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001102657.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF836 | NM_001102657.3 | c.2390G>A | p.Arg797Gln | missense_variant | Exon 5 of 5 | ENST00000682614.1 | NP_001096127.1 | |
ZNF836 | XM_011526558.4 | c.2390G>A | p.Arg797Gln | missense_variant | Exon 5 of 5 | XP_011524860.1 | ||
ZNF836 | XM_011526559.4 | c.2390G>A | p.Arg797Gln | missense_variant | Exon 4 of 4 | XP_011524861.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF836 | ENST00000682614.1 | c.2390G>A | p.Arg797Gln | missense_variant | Exon 5 of 5 | NM_001102657.3 | ENSP00000507838.1 | |||
ZNF836 | ENST00000597252.5 | c.2390G>A | p.Arg797Gln | missense_variant | Exon 5 of 5 | 2 | ENSP00000470239.1 | |||
ENSG00000267827 | ENST00000594362.1 | n.554+5172G>A | intron_variant | Intron 4 of 4 | 5 | |||||
ENSG00000267827 | ENST00000598982.5 | n.494+5172G>A | intron_variant | Intron 4 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000659 AC: 10AN: 151846Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000798 AC: 20AN: 250594Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135650
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461534Hom.: 1 Cov.: 34 AF XY: 0.0000798 AC XY: 58AN XY: 727072
GnomAD4 genome AF: 0.0000658 AC: 10AN: 151962Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2390G>A (p.R797Q) alteration is located in exon 5 (coding exon 3) of the ZNF836 gene. This alteration results from a G to A substitution at nucleotide position 2390, causing the arginine (R) at amino acid position 797 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at