chr13-32078842-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_023037.3(FRY):c.79G>A(p.Val27Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000281 in 1,613,614 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.00093 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 0 hom. )
Consequence
FRY
NM_023037.3 missense
NM_023037.3 missense
Scores
1
4
8
Clinical Significance
Conservation
PhyloP100: 9.32
Genes affected
FRY (HGNC:20367): (FRY microtubule binding protein) Predicted to enable enzyme inhibitor activity. Predicted to be involved in cell morphogenesis and neuron projection development. Predicted to be located in microtubule organizing center and spindle pole. Predicted to be active in cell cortex and site of polarized growth. [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.
PP2
?
Missense variant where missense usually causes diseases, FRY
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0094097555).
BP6
?
Variant 13-32078842-G-A is Benign according to our data. Variant chr13-32078842-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 738354.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 140 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRY | NM_023037.3 | c.79G>A | p.Val27Ile | missense_variant | 2/61 | ENST00000542859.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRY | ENST00000542859.6 | c.79G>A | p.Val27Ile | missense_variant | 2/61 | 5 | NM_023037.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000921 AC: 140AN: 152034Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000425 AC: 106AN: 249508Hom.: 0 AF XY: 0.000414 AC XY: 56AN XY: 135370
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GnomAD4 exome AF: 0.000213 AC: 312AN: 1461462Hom.: 0 Cov.: 31 AF XY: 0.000201 AC XY: 146AN XY: 727068
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GnomAD4 genome ? AF: 0.000927 AC: 141AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.000887 AC XY: 66AN XY: 74376
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Uncertain
T
Polyphen
0.19
.;.;.;B;.
Vest4
0.39, 0.69
MVP
0.10
MPC
0.38
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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