3-99848393-A-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001387850.1(FILIP1L):āc.3283T>Cā(p.Leu1095=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000438 in 1,461,876 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.000044 ( 2 hom. )
Consequence
FILIP1L
NM_001387850.1 synonymous
NM_001387850.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.758
Genes affected
FILIP1L (HGNC:24589): (filamin A interacting protein 1 like) Predicted to be located in cytoplasm; membrane; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant 3-99848393-A-G is Benign according to our data. Variant chr3-99848393-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3057961.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.758 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FILIP1L | NM_001387850.1 | c.3283T>C | p.Leu1095= | synonymous_variant | 5/6 | ENST00000477258.2 | |
CMSS1 | NM_032359.4 | c.64+30350A>G | intron_variant | ENST00000421999.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FILIP1L | ENST00000477258.2 | c.3283T>C | p.Leu1095= | synonymous_variant | 5/6 | 2 | NM_001387850.1 | P4 | |
CMSS1 | ENST00000421999.8 | c.64+30350A>G | intron_variant | 1 | NM_032359.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
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GnomAD3 exomes AF: 0.000160 AC: 40AN: 249528Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135372
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GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461876Hom.: 2 Cov.: 33 AF XY: 0.0000523 AC XY: 38AN XY: 727238
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FILIP1L-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 24, 2019 | 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). - |
Computational scores
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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