rs1366842
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_194250.2(ZNF804A):c.2120C>A(p.Thr707Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 1,607,472 control chromosomes in the GnomAD database, including 273,663 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_194250.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF804A | NM_194250.2 | c.2120C>A | p.Thr707Lys | missense_variant | 4/4 | ENST00000302277.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF804A | ENST00000302277.7 | c.2120C>A | p.Thr707Lys | missense_variant | 4/4 | 1 | NM_194250.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.474 AC: 72074AN: 151958Hom.: 20721 Cov.: 33
GnomAD3 exomes AF: 0.593 AC: 144400AN: 243692Hom.: 45977 AF XY: 0.591 AC XY: 78077AN XY: 132160
GnomAD4 exome AF: 0.581 AC: 846302AN: 1455396Hom.: 252944 Cov.: 43 AF XY: 0.581 AC XY: 420564AN XY: 723870
GnomAD4 genome AF: 0.474 AC: 72073AN: 152076Hom.: 20719 Cov.: 33 AF XY: 0.480 AC XY: 35700AN XY: 74350
ClinVar
Submissions by phenotype
ZNF804A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at