chr6-75312516-C-G
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_015687.5(FILIP1):c.3316G>C(p.Gly1106Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000477 in 1,614,116 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 Benign (no stars).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000036 ( 0 hom. )
Consequence
FILIP1
NM_015687.5 missense
NM_015687.5 missense
Scores
4
8
7
Clinical Significance
Conservation
PhyloP100: 6.17
Genes affected
FILIP1 (HGNC:21015): (filamin A interacting protein 1) This gene encodes a filamin A binding protein. The encoded protein promotes the degradation of filamin A and may regulate cortical neuron migration and dendritic spine morphology. Mice lacking a functional copy of this gene exhibit reduced dendritic spine length and altered excitatory signaling. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.17751008).
BP6
Variant 6-75312516-C-G is Benign according to our data. Variant chr6-75312516-C-G is described in ClinVar as [Benign]. Clinvar id is 208956.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FILIP1 | NM_015687.5 | c.3316G>C | p.Gly1106Arg | missense_variant | 5/6 | ENST00000237172.12 | NP_056502.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FILIP1 | ENST00000237172.12 | c.3316G>C | p.Gly1106Arg | missense_variant | 5/6 | 1 | NM_015687.5 | ENSP00000237172 | P4 | |
TMEM30A-DT | ENST00000661161.1 | n.445C>G | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152116Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251476Hom.: 0 AF XY: 0.0000956 AC XY: 13AN XY: 135914
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GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461882Hom.: 0 Cov.: 35 AF XY: 0.0000330 AC XY: 24AN XY: 727242
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GnomAD4 genome AF: 0.000158 AC: 24AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Abnormality of neuronal migration Benign:1
Benign, no assertion criteria provided | clinical testing | Génétique et pathophysiologie de maladies neurodéveloppementales et épileptogènes, Institut de génétique et de biologie moléculaire et cellulaire | Oct 31, 2014 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Pathogenic
DEOGEN2
Benign
.;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
D;D;.
Vest4
MVP
MPC
0.78
ClinPred
T
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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