7-128850372-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001458.5(FLNC):c.5299-12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,486 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 (★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_001458.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLNC | NM_001458.5 | c.5299-12C>T | intron_variant | Intron 31 of 47 | ENST00000325888.13 | NP_001449.3 | ||
FLNC | NM_001127487.2 | c.5200-12C>T | intron_variant | Intron 30 of 46 | NP_001120959.1 | |||
FLNC-AS1 | NR_149055.1 | n.349G>A | non_coding_transcript_exon_variant | Exon 4 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLNC | ENST00000325888.13 | c.5299-12C>T | intron_variant | Intron 31 of 47 | 1 | NM_001458.5 | ENSP00000327145.8 | |||
FLNC | ENST00000346177.6 | c.5200-12C>T | intron_variant | Intron 30 of 46 | 1 | ENSP00000344002.6 | ||||
FLNC-AS1 | ENST00000469965.1 | n.349G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249322Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135296
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457486Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 725458
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Myofibrillar myopathy 5;C3279722:Distal myopathy with posterior leg and anterior hand involvement;C4310749:Hypertrophic cardiomyopathy 26;CN239310:Dilated Cardiomyopathy, Dominant Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at