chr4-80286487-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004464.4(FGF5):c.622C>A(p.Pro208Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004464.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGF5 | NM_004464.4 | c.622C>A | p.Pro208Thr | missense_variant | 3/3 | ENST00000312465.12 | |
FGF5 | NM_001291812.2 | c.193C>A | p.Pro65Thr | missense_variant | 3/3 | ||
FGF5 | NM_033143.2 | c.*146C>A | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF5 | ENST00000312465.12 | c.622C>A | p.Pro208Thr | missense_variant | 3/3 | 1 | NM_004464.4 | P1 | |
FGF5 | ENST00000456523.3 | c.*146C>A | 3_prime_UTR_variant | 2/2 | 1 | ||||
FGF5 | ENST00000503413.1 | n.571C>A | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
FGF5 | ENST00000507780.1 | c.342+11475C>A | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461802Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727202
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.622C>A (p.P208T) alteration is located in exon 3 (coding exon 3) of the FGF5 gene. This alteration results from a C to A substitution at nucleotide position 622, causing the proline (P) at amino acid position 208 to be replaced by a threonine (T). 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