chr6-167004399-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007045.4(CEP43):c.436G>A(p.Glu146Lys) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000419 in 1,432,134 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007045.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP43 | NM_007045.4 | c.436G>A | p.Glu146Lys | missense_variant, splice_region_variant | 5/13 | ENST00000366847.9 | |
CEP43 | NM_194429.3 | c.436G>A | p.Glu146Lys | missense_variant, splice_region_variant | 5/12 | ||
CEP43 | NM_001278690.2 | c.436G>A | p.Glu146Lys | missense_variant, splice_region_variant | 5/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP43 | ENST00000366847.9 | c.436G>A | p.Glu146Lys | missense_variant, splice_region_variant | 5/13 | 1 | NM_007045.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000870 AC: 2AN: 229946Hom.: 0 AF XY: 0.00000803 AC XY: 1AN XY: 124474
GnomAD4 exome AF: 0.00000419 AC: 6AN: 1432134Hom.: 0 Cov.: 30 AF XY: 0.00000421 AC XY: 3AN XY: 712206
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 27, 2022 | The c.436G>A (p.E146K) 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 436, causing the glutamic acid (E) at amino acid position 146 to be replaced by a lysine (K). 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