chr4-1804435-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 4P and 3B. PM1PM2BP4_ModerateBP6
The NM_000142.5(FGFR3):c.1181C>T(p.Thr394Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,612,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T394T) has been classified as Likely benign.
Frequency
Consequence
NM_000142.5 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 |
---|---|---|---|---|---|---|---|
FGFR3 | NM_000142.5 | c.1181C>T | p.Thr394Met | missense_variant | 9/18 | ENST00000440486.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGFR3 | ENST00000440486.8 | c.1181C>T | p.Thr394Met | missense_variant | 9/18 | 5 | NM_000142.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152240Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000602 AC: 15AN: 249302Hom.: 0 AF XY: 0.0000667 AC XY: 9AN XY: 134834
GnomAD4 exome AF: 0.000150 AC: 219AN: 1460008Hom.: 0 Cov.: 35 AF XY: 0.000145 AC XY: 105AN XY: 726322
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152240Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74380
ClinVar
Submissions by phenotype
Classic Hodgkin lymphoma Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Pathology Department, Puerta del Mar University Hospital | Oct 01, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at