chr11-92353483-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001367949.2(FAT3):c.1371G>A(p.Gln457=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0574 in 1,613,216 control chromosomes in the GnomAD database, including 3,275 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.074 ( 579 hom., cov: 32)
Exomes 𝑓: 0.056 ( 2696 hom. )
Consequence
FAT3
NM_001367949.2 synonymous
NM_001367949.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.330
Genes affected
FAT3 (HGNC:23112): (FAT atypical cadherin 3) Predicted to enable calcium ion binding activity. Predicted to be involved in cell-cell adhesion. Predicted to act upstream of or within several processes, including negative regulation of dendrite development; neuron migration; and retina layer formation. Predicted to be located in dendrite and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 11-92353483-G-A is Benign according to our data. Variant chr11-92353483-G-A is described in ClinVar as [Benign]. Clinvar id is 3056107.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.33 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAT3 | NM_001367949.2 | c.1371G>A | p.Gln457= | synonymous_variant | 2/28 | ENST00000525166.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAT3 | ENST00000525166.6 | c.1371G>A | p.Gln457= | synonymous_variant | 2/28 | 5 | NM_001367949.2 | ||
FAT3 | ENST00000409404.6 | c.1371G>A | p.Gln457= | synonymous_variant | 1/25 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0745 AC: 11329AN: 152042Hom.: 576 Cov.: 32
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GnomAD3 exomes AF: 0.0455 AC: 11241AN: 247038Hom.: 423 AF XY: 0.0431 AC XY: 5774AN XY: 133944
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GnomAD4 exome AF: 0.0557 AC: 81315AN: 1461056Hom.: 2696 Cov.: 32 AF XY: 0.0537 AC XY: 39036AN XY: 726728
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GnomAD4 genome ? AF: 0.0744 AC: 11328AN: 152160Hom.: 579 Cov.: 32 AF XY: 0.0720 AC XY: 5352AN XY: 74380
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FAT3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 09, 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
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at