5-73051352-A-T
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_138782.3(FCHO2):c.943A>T(p.Ile315Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000021 in 1,527,166 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000019 ( 1 hom. )
Consequence
FCHO2
NM_138782.3 missense
NM_138782.3 missense
Scores
3
16
Clinical Significance
Conservation
PhyloP100: 2.83
Genes affected
FCHO2 (HGNC:25180): (FCH and mu domain containing endocytic adaptor 2) Enables identical protein binding activity. Involved in clathrin coat assembly and clathrin-dependent endocytosis. Located in clathrin-coated pit and clathrin-coated vesicle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.013338417).
BS2
High AC in GnomAd4 at 6 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FCHO2 | ENST00000430046.7 | c.943A>T | p.Ile315Phe | missense_variant | 12/26 | 1 | NM_138782.3 | ENSP00000393776.2 | ||
FCHO2 | ENST00000512348.5 | c.844A>T | p.Ile282Phe | missense_variant | 11/25 | 2 | ENSP00000427296.1 | |||
FCHO2 | ENST00000503302.1 | n.253A>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151980Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000133 AC: 20AN: 150200Hom.: 1 AF XY: 0.000176 AC XY: 14AN XY: 79322
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GnomAD4 exome AF: 0.0000189 AC: 26AN: 1375186Hom.: 1 Cov.: 27 AF XY: 0.0000221 AC XY: 15AN XY: 678988
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GnomAD4 genome AF: 0.0000395 AC: 6AN: 151980Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74232
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.943A>T (p.I315F) alteration is located in exon 12 (coding exon 12) of the FCHO2 gene. This alteration results from a A to T substitution at nucleotide position 943, causing the isoleucine (I) at amino acid position 315 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MutPred
Gain of catalytic residue at I315 (P = 0.2818);.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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