rs201335006
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000325888.13(FLNC):c.5540-6C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,613,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000325888.13 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLNC | NM_001458.5 | c.5540-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000325888.13 | NP_001449.3 | |||
FLNC-AS1 | NR_149055.1 | n.315+175G>T | intron_variant, non_coding_transcript_variant | |||||
FLNC | NM_001127487.2 | c.5441-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_001120959.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLNC | ENST00000325888.13 | c.5540-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001458.5 | ENSP00000327145 | P3 | |||
FLNC | ENST00000346177.6 | c.5441-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000344002 | A1 | ||||
FLNC-AS1 | ENST00000469965.1 | n.315+175G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249302Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135296
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461706Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727156
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74452
ClinVar
Submissions by phenotype
FLNC-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 12, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Myofibrillar myopathy 5;C3279722:Distal myopathy with posterior leg and anterior hand involvement;C4310749:Hypertrophic cardiomyopathy 26;CN239310:Dilated Cardiomyopathy, Dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at