chr6-167004298-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007045.4(CEP43):c.335G>A(p.Arg112Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000529 in 1,608,290 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007045.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP43 | NM_007045.4 | c.335G>A | p.Arg112Gln | missense_variant | 5/13 | ENST00000366847.9 | |
CEP43 | NM_194429.3 | c.335G>A | p.Arg112Gln | missense_variant | 5/12 | ||
CEP43 | NM_001278690.2 | c.335G>A | p.Arg112Gln | missense_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP43 | ENST00000366847.9 | c.335G>A | p.Arg112Gln | missense_variant | 5/13 | 1 | NM_007045.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152072Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000765 AC: 19AN: 248358Hom.: 0 AF XY: 0.0000819 AC XY: 11AN XY: 134304
GnomAD4 exome AF: 0.0000350 AC: 51AN: 1456100Hom.: 0 Cov.: 30 AF XY: 0.0000387 AC XY: 28AN XY: 724412
GnomAD4 genome AF: 0.000223 AC: 34AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74412
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.335G>A (p.R112Q) alteration is located in exon 5 (coding exon 5) of the FGFR1OP gene. This alteration results from a G to A substitution at nucleotide position 335, causing the arginine (R) at amino acid position 112 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at