12-124314355-GC-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001365156.1(RFLNA):c.484del(p.Leu162CysfsTer111) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
RFLNA
NM_001365156.1 frameshift
NM_001365156.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.44
Genes affected
RFLNA (HGNC:27051): (refilin A) Predicted to enable filamin binding activity. Predicted to be involved in several processes, including actin filament bundle organization; negative regulation of bone mineralization involved in bone maturation; and negative regulation of chondrocyte development. Predicted to be located in cytoplasm. Predicted to be active in actin filament bundle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| RFLNA | NM_001365156.1 | c.484del | p.Leu162CysfsTer111 | frameshift_variant | 3/3 | ENST00000546355.4 | NP_001352085.1 | |
| ZNF664-RFLNA | NM_001204299.3 | c.241del | p.Leu81CysfsTer111 | frameshift_variant | 5/5 | NP_001191228.1 | ||
| ZNF664-RFLNA | NM_001347902.2 | c.241del | p.Leu81CysfsTer111 | frameshift_variant | 5/5 | NP_001334831.1 | ||
| RFLNA | NM_181709.5 | c.241del | p.Leu81CysfsTer111 | frameshift_variant | 3/3 | NP_859060.3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| RFLNA | ENST00000546355.4 | c.484del | p.Leu162CysfsTer111 | frameshift_variant | 3/3 | 1 | NM_001365156.1 | ENSP00000444080 | P1 | |
| RFLNA | ENST00000338359.4 | c.241del | p.Leu81CysfsTer? | frameshift_variant | 2/2 | 1 | ENSP00000345898 | |||
| RFLNA | ENST00000324038.6 | c.241del | p.Leu81CysfsTer111 | frameshift_variant | 3/3 | 2 | ENSP00000315626 | |||
| RFLNA | ENST00000389727.8 | c.241del | p.Leu81CysfsTer111 | frameshift_variant | 5/5 | 5 | ENSP00000374377 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Uncertain:1
| Uncertain significance, no assertion criteria provided | literature only | OMIM | Dec 20, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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
Publications
No publications associated with this variant yet.