chr5-177091036-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_213647.3(FGFR4):c.535A>G(p.Thr179Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,610,462 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_213647.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGFR4 | NM_213647.3 | c.535A>G | p.Thr179Ala | missense_variant | 5/18 | ENST00000292408.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGFR4 | ENST00000292408.9 | c.535A>G | p.Thr179Ala | missense_variant | 5/18 | 1 | NM_213647.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00122 AC: 186AN: 152110Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00275 AC: 690AN: 250730Hom.: 10 AF XY: 0.00261 AC XY: 354AN XY: 135552
GnomAD4 exome AF: 0.00106 AC: 1541AN: 1458234Hom.: 18 Cov.: 33 AF XY: 0.00105 AC XY: 760AN XY: 724546
GnomAD4 genome ? AF: 0.00121 AC: 184AN: 152228Hom.: 4 Cov.: 32 AF XY: 0.00150 AC XY: 112AN XY: 74430
ClinVar
Submissions by phenotype
FGFR4-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 28, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at