chr19-52950567-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001202457.3(ZNF816):āc.1208A>Cā(p.Asp403Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,620 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 (ā ).
Frequency
Consequence
NM_001202457.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF816 | NM_001202457.3 | c.1208A>C | p.Asp403Ala | missense_variant | 4/4 | ENST00000444460.7 | NP_001189386.1 | |
ZNF816-ZNF321P | NM_001202473.2 | c.190+2184A>C | intron_variant | NP_001189402.1 | ||||
ZNF816 | NM_001031665.4 | c.1208A>C | p.Asp403Ala | missense_variant | 5/5 | NP_001026835.1 | ||
ZNF816 | NM_001202456.3 | c.1208A>C | p.Asp403Ala | missense_variant | 4/4 | NP_001189385.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF816 | ENST00000444460.7 | c.1208A>C | p.Asp403Ala | missense_variant | 4/4 | 1 | NM_001202457.3 | ENSP00000403266 | P1 | |
ZNF816 | ENST00000357666.8 | c.1208A>C | p.Asp403Ala | missense_variant | 5/5 | 1 | ENSP00000350295 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151780Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251372Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135866
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461840Hom.: 0 Cov.: 64 AF XY: 0.0000179 AC XY: 13AN XY: 727216
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151780Hom.: 0 Cov.: 33 AF XY: 0.0000405 AC XY: 3AN XY: 74102
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.1208A>C (p.D403A) alteration is located in exon 5 (coding exon 3) of the ZNF816 gene. This alteration results from a A to C substitution at nucleotide position 1208, causing the aspartic acid (D) at amino acid position 403 to be replaced by an alanine (A). 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