rs753520867
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 4P and 9B. PM1PM2BP4_StrongBP6BS1
The NM_000142.5(FGFR3):c.967G>A(p.Val323Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,613,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000142.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGFR3 | NM_000142.5 | c.967G>A | p.Val323Ile | missense_variant | 8/18 | ENST00000440486.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGFR3 | ENST00000440486.8 | c.967G>A | p.Val323Ile | missense_variant | 8/18 | 5 | NM_000142.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152248Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000172 AC: 43AN: 250646Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135810
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461664Hom.: 0 Cov.: 33 AF XY: 0.0000206 AC XY: 15AN XY: 727150
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152248Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 25, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 14, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 15, 2021 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | The c.967G>A (p.V323I) alteration is located in exon 8 (coding exon 7) of the FGFR3 gene. This alteration results from a G to A substitution at nucleotide position 967, causing the valine (V) at amino acid position 323 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
FGFR3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 01, 2021 | This variant is classified as likely 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