chr19-57754093-A-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_173632.4(ZNF776):āc.963A>Cā(p.Glu321Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,606,846 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_173632.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF776 | NM_173632.4 | c.963A>C | p.Glu321Asp | missense_variant | 3/3 | ENST00000317178.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF776 | ENST00000317178.10 | c.963A>C | p.Glu321Asp | missense_variant | 3/3 | 1 | NM_173632.4 | P1 | |
ZNF776 | ENST00000451849.1 | c.109-2779A>C | intron_variant | 3 | |||||
ZNF776 | ENST00000489376.1 | n.50A>C | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000124 AC: 18AN: 144932Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000390 AC: 98AN: 251432Hom.: 2 AF XY: 0.000302 AC XY: 41AN XY: 135890
GnomAD4 exome AF: 0.000135 AC: 198AN: 1461778Hom.: 2 Cov.: 32 AF XY: 0.000135 AC XY: 98AN XY: 727198
GnomAD4 genome AF: 0.000124 AC: 18AN: 145068Hom.: 0 Cov.: 33 AF XY: 0.000113 AC XY: 8AN XY: 70846
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.963A>C (p.E321D) alteration is located in exon 3 (coding exon 3) of the ZNF776 gene. This alteration results from a A to C substitution at nucleotide position 963, causing the glutamic acid (E) at amino acid position 321 to be replaced by an aspartic acid (D). 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