chr19-3530839-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_016263.4(FZR1):c.702C>T(p.Ser234Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000539 in 1,612,790 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00036 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00056 ( 9 hom. )
Consequence
FZR1
NM_016263.4 synonymous
NM_016263.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.58
Genes affected
FZR1 (HGNC:24824): (fizzy and cell division cycle 20 related 1) Predicted to enable anaphase-promoting complex binding activity and ubiquitin ligase activator activity. Involved in anaphase-promoting complex-dependent catabolic process; mitotic G2 DNA damage checkpoint signaling; and positive regulation of protein metabolic process. Located in nuclear membrane and nucleoplasm. Colocalizes with anaphase-promoting complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 19-3530839-C-T is Benign according to our data. Variant chr19-3530839-C-T is described in ClinVar as [Benign]. Clinvar id is 3025329.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-4.58 with no splicing effect.
BS2
High AC in GnomAd4 at 55 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FZR1 | NM_016263.4 | c.702C>T | p.Ser234Ser | synonymous_variant | Exon 8 of 14 | ENST00000441788.7 | NP_057347.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000368 AC: 56AN: 152032Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00109 AC: 270AN: 248732Hom.: 4 AF XY: 0.00155 AC XY: 209AN XY: 134848
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GnomAD4 exome AF: 0.000557 AC: 814AN: 1460640Hom.: 9 Cov.: 30 AF XY: 0.000801 AC XY: 582AN XY: 726602
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GnomAD4 genome AF: 0.000361 AC: 55AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.000538 AC XY: 40AN XY: 74378
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
FZR1: BP4, BP7, BS1, BS2 -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at