NM_023037.3:c.1233T>C
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_023037.3(FRY):c.1233T>C(p.Leu411Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Consequence
FRY
NM_023037.3 synonymous
NM_023037.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.41
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
Variant 13-32147335-T-C is Benign according to our data. Variant chr13-32147335-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 747924.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.41 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRY | ENST00000542859.6 | c.1233T>C | p.Leu411Leu | synonymous_variant | Exon 12 of 61 | 5 | NM_023037.3 | ENSP00000445043.2 | ||
FRY | ENST00000647500.1 | c.1368T>C | p.Leu456Leu | synonymous_variant | Exon 12 of 61 | ENSP00000494761.1 | ||||
FRY | ENST00000642040.1 | c.1233T>C | p.Leu411Leu | synonymous_variant | Exon 12 of 62 | ENSP00000493189.1 | ||||
FRY | ENST00000645780.1 | c.1083T>C | p.Leu361Leu | synonymous_variant | Exon 13 of 62 | ENSP00000494080.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 29
GnomAD4 exome
Cov.:
29
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 13, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at