rs121909637
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_023110.3(FGFR1):c.1409G>T(p.Arg470Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,188 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R470C) has been classified as Uncertain significance.
Frequency
Consequence
NM_023110.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGFR1 | NM_023110.3 | c.1409G>T | p.Arg470Leu | missense_variant | 10/18 | ENST00000447712.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGFR1 | ENST00000447712.7 | c.1409G>T | p.Arg470Leu | missense_variant | 10/18 | 1 | NM_023110.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249552Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135392
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727230
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74486
ClinVar
Submissions by phenotype
Hypogonadotropic hypogonadism 2 with or without anosmia Pathogenic:1Other:1
Likely pathogenic, criteria provided, single submitter | research | Reproductive Endocrine Unit, Massachusetts General Hospital | May 04, 2023 | The variant has been classified as LP3 based on the variant meeting the following ACMG Criteria: PS3,PP2,PP4. - |
risk factor, no assertion criteria provided | literature only | OMIM | Feb 01, 2007 | - - |
Pfeiffer syndrome;C1563720:Hypogonadotropic hypogonadism 2 with or without anosmia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at