rs113618587
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_001458.5(FLNC):c.6459C>A(p.Thr2153=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,332 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T2153T) has been classified as Benign.
Frequency
Consequence
NM_001458.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNC | NM_001458.5 | c.6459C>A | p.Thr2153= | synonymous_variant | 39/48 | ENST00000325888.13 | |
FLNC-AS1 | NR_149055.1 | n.103-415G>T | intron_variant, non_coding_transcript_variant | ||||
FLNC | NM_001127487.2 | c.6360C>A | p.Thr2120= | synonymous_variant | 38/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNC | ENST00000325888.13 | c.6459C>A | p.Thr2153= | synonymous_variant | 39/48 | 1 | NM_001458.5 | P3 | |
FLNC | ENST00000346177.6 | c.6360C>A | p.Thr2120= | synonymous_variant | 38/47 | 1 | A1 | ||
FLNC-AS1 | ENST00000469965.1 | n.103-415G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249188Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135300
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461332Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 726990
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
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at