2-184936178-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_194250.2(ZNF804A):c.782A>T(p.Gln261Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 1,613,750 control chromosomes in the GnomAD database, including 322,495 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF804A | NM_194250.2 | c.782A>T | p.Gln261Leu | missense_variant | 4/4 | ENST00000302277.7 | NP_919226.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF804A | ENST00000302277.7 | c.782A>T | p.Gln261Leu | missense_variant | 4/4 | 1 | NM_194250.2 | ENSP00000303252 | P1 |
Frequencies
GnomAD3 genomes AF: 0.599 AC: 90997AN: 151928Hom.: 27995 Cov.: 32
GnomAD3 exomes AF: 0.656 AC: 164749AN: 251092Hom.: 55061 AF XY: 0.653 AC XY: 88576AN XY: 135704
GnomAD4 exome AF: 0.632 AC: 924106AN: 1461704Hom.: 294493 Cov.: 64 AF XY: 0.632 AC XY: 459796AN XY: 727142
GnomAD4 genome AF: 0.599 AC: 91041AN: 152046Hom.: 28002 Cov.: 32 AF XY: 0.603 AC XY: 44784AN XY: 74294
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2020 | This variant is associated with the following publications: (PMID: 24315717) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at