rs1554401403
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP2PP3PP5_Moderate
The NM_001458.5(FLNC):c.6892C>T(p.Pro2298Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,456,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P2298L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001458.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLNC | NM_001458.5 | c.6892C>T | p.Pro2298Ser | missense_variant | 41/48 | ENST00000325888.13 | NP_001449.3 | |
FLNC | NM_001127487.2 | c.6793C>T | p.Pro2265Ser | missense_variant | 40/47 | NP_001120959.1 | ||
FLNC-AS1 | NR_149055.1 | n.103-1180G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLNC | ENST00000325888.13 | c.6892C>T | p.Pro2298Ser | missense_variant | 41/48 | 1 | NM_001458.5 | ENSP00000327145.8 | ||
FLNC | ENST00000346177.6 | c.6793C>T | p.Pro2265Ser | missense_variant | 40/47 | 1 | ENSP00000344002.6 | |||
FLNC-AS1 | ENST00000469965.1 | n.103-1180G>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1456954Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 724496
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Restrictive cardiomyopathy Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Institute Of Molecular Biology And Genetics, Federal Almazov National Medical Research Centre | May 23, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at