11-69810396-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_005247.4(FGF3):c.629G>A(p.Arg210Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000223 in 1,559,512 control chromosomes in the GnomAD database, including 4 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 Likely benign (★★).
Frequency
Consequence
NM_005247.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FGF3 | NM_005247.4 | c.629G>A | p.Arg210Gln | missense_variant | Exon 3 of 3 | ENST00000334134.4 | NP_005238.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000401 AC: 61AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000704 AC: 134AN: 190240Hom.: 3 AF XY: 0.000666 AC XY: 69AN XY: 103540
GnomAD4 exome AF: 0.000205 AC: 288AN: 1407194Hom.: 4 Cov.: 30 AF XY: 0.000202 AC XY: 140AN XY: 692884
GnomAD4 genome AF: 0.000394 AC: 60AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.000457 AC XY: 34AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:2
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FGF3-related disorder Benign:1
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