9-133064661-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001807.6(CEL):c.239T>C(p.Phe80Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000271 in 1,613,868 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F80L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001807.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEL | NM_001807.6 | c.239T>C | p.Phe80Ser | missense_variant | 3/11 | ENST00000372080.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEL | ENST00000372080.8 | c.239T>C | p.Phe80Ser | missense_variant | 3/11 | 5 | NM_001807.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152036Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000582 AC: 145AN: 249244Hom.: 1 AF XY: 0.000710 AC XY: 96AN XY: 135294
GnomAD4 exome AF: 0.000278 AC: 406AN: 1461712Hom.: 5 Cov.: 32 AF XY: 0.000385 AC XY: 280AN XY: 727132
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152156Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74410
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 27, 2022 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at