20-23364479-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_022482.5(GZF1):c.96C>T(p.Asp32Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,614,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_022482.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GZF1 | ENST00000338121.10 | c.96C>T | p.Asp32Asp | synonymous_variant | Exon 2 of 6 | 1 | NM_022482.5 | ENSP00000338290.5 | ||
GZF1 | ENST00000377051.2 | c.96C>T | p.Asp32Asp | synonymous_variant | Exon 1 of 5 | 1 | ENSP00000366250.2 | |||
GZF1 | ENST00000424216.1 | c.96C>T | p.Asp32Asp | synonymous_variant | Exon 3 of 3 | 5 | ENSP00000410009.1 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251414Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135870
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461858Hom.: 0 Cov.: 32 AF XY: 0.0000440 AC XY: 32AN XY: 727228
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74504
ClinVar
Submissions by phenotype
GZF1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at