17-45241901-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005892.4(FMNL1):c.1640C>A(p.Pro547Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000416 in 1,418,192 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 Uncertain significance (★).
Frequency
Consequence
NM_005892.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FMNL1 | NM_005892.4 | c.1640C>A | p.Pro547Gln | missense_variant | Exon 15 of 27 | ENST00000331495.8 | NP_005883.3 | |
FMNL1 | NM_001411128.1 | c.1640C>A | p.Pro547Gln | missense_variant | Exon 15 of 26 | NP_001398057.1 | ||
FMNL1-AS1 | NR_186807.1 | n.-131G>T | upstream_gene_variant | |||||
FMNL1-AS1 | NR_186808.1 | n.-131G>T | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FMNL1 | ENST00000331495.8 | c.1640C>A | p.Pro547Gln | missense_variant | Exon 15 of 27 | 1 | NM_005892.4 | ENSP00000329219.2 | ||
FMNL1 | ENST00000587489.6 | c.1640C>A | p.Pro547Gln | missense_variant | Exon 15 of 26 | 1 | ENSP00000465474.2 | |||
FMNL1 | ENST00000587856.1 | n.2209C>A | non_coding_transcript_exon_variant | Exon 7 of 16 | 2 | |||||
FMNL1-AS1 | ENST00000587534.1 | n.-167G>T | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151404Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000347 AC: 1AN: 28850Hom.: 0 AF XY: 0.0000591 AC XY: 1AN XY: 16928
GnomAD4 exome AF: 0.0000426 AC: 54AN: 1266788Hom.: 0 Cov.: 35 AF XY: 0.0000419 AC XY: 26AN XY: 620496
GnomAD4 genome AF: 0.0000330 AC: 5AN: 151404Hom.: 0 Cov.: 32 AF XY: 0.0000406 AC XY: 3AN XY: 73868
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1640C>A (p.P547Q) alteration is located in exon 15 (coding exon 15) of the FMNL1 gene. This alteration results from a C to A substitution at nucleotide position 1640, causing the proline (P) at amino acid position 547 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at