rs146662137
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The ENST00000481110.7(FGFR3):c.2191C>T(p.Arg731Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,609,292 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000481110.7 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 |
---|---|---|---|---|---|---|---|
FGFR3 | NM_000142.5 | c.2259C>T | p.Thr753= | synonymous_variant | 17/18 | ENST00000440486.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGFR3 | ENST00000440486.8 | c.2259C>T | p.Thr753= | synonymous_variant | 17/18 | 5 | NM_000142.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152104Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000717 AC: 17AN: 237200Hom.: 0 AF XY: 0.0000464 AC XY: 6AN XY: 129382
GnomAD4 exome AF: 0.000107 AC: 156AN: 1457070Hom.: 0 Cov.: 36 AF XY: 0.0000952 AC XY: 69AN XY: 724566
GnomAD4 genome AF: 0.000151 AC: 23AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74420
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 26, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at