19-55593325-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032836.3(FIZ1):c.616G>A(p.Ala206Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000148 in 1,282,356 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_032836.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FIZ1 | NM_032836.3 | c.616G>A | p.Ala206Thr | missense_variant | 3/3 | ENST00000221665.5 | NP_116225.2 | |
FIZ1 | XM_005259352.5 | c.616G>A | p.Ala206Thr | missense_variant | 3/3 | XP_005259409.1 | ||
FIZ1 | XM_047439564.1 | c.616G>A | p.Ala206Thr | missense_variant | 2/2 | XP_047295520.1 | ||
FIZ1 | XM_011527426.3 | c.598G>A | p.Ala200Thr | missense_variant | 2/2 | XP_011525728.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000267 AC: 4AN: 150028Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000132 AC: 15AN: 1132328Hom.: 0 Cov.: 33 AF XY: 0.00000914 AC XY: 5AN XY: 547026
GnomAD4 genome AF: 0.0000267 AC: 4AN: 150028Hom.: 0 Cov.: 32 AF XY: 0.0000547 AC XY: 4AN XY: 73192
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 13, 2023 | The c.616G>A (p.A206T) alteration is located in exon 3 (coding exon 2) of the FIZ1 gene. This alteration results from a G to A substitution at nucleotide position 616, causing the alanine (A) at amino acid position 206 to be replaced by a threonine (T). 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