chr19-57253316-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001023563.4(ZNF805):c.497G>A(p.Ser166Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000425 in 1,575,468 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_001023563.4 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 |
---|---|---|---|---|---|---|---|
ZNF805 | NM_001023563.4 | c.497G>A | p.Ser166Asn | missense_variant | 4/4 | ENST00000414468.3 | |
ZNF805 | NM_001145078.2 | c.98G>A | p.Ser33Asn | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF805 | ENST00000414468.3 | c.497G>A | p.Ser166Asn | missense_variant | 4/4 | 5 | NM_001023563.4 | P1 | |
ZNF805 | ENST00000354309.4 | c.98G>A | p.Ser33Asn | missense_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152262Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000262 AC: 5AN: 190794Hom.: 0 AF XY: 0.0000196 AC XY: 2AN XY: 102060
GnomAD4 exome AF: 0.0000464 AC: 66AN: 1423206Hom.: 0 Cov.: 30 AF XY: 0.0000383 AC XY: 27AN XY: 704212
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.497G>A (p.S166N) alteration is located in exon 4 (coding exon 4) of the ZNF805 gene. This alteration results from a G to A substitution at nucleotide position 497, causing the serine (S) at amino acid position 166 to be replaced by an asparagine (N). 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