16-55849626-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001143685.2(CES5A):āc.1421T>Cā(p.Phe474Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,806 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 (ā ).
Frequency
Consequence
NM_001143685.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CES5A | NM_001143685.2 | c.1421T>C | p.Phe474Ser | missense_variant, splice_region_variant | 11/13 | ENST00000290567.14 | NP_001137157.1 | |
CES5A | NM_001190158.1 | c.1508T>C | p.Phe503Ser | missense_variant, splice_region_variant | 12/14 | NP_001177087.1 | ||
CES5A | NM_145024.3 | c.1274-2786T>C | intron_variant | NP_659461.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CES5A | ENST00000290567.14 | c.1421T>C | p.Phe474Ser | missense_variant, splice_region_variant | 11/13 | 1 | NM_001143685.2 | ENSP00000290567.9 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248692Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135130
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461640Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727090
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.1508T>C (p.F503S) alteration is located in exon 12 (coding exon 12) of the CES5A gene. This alteration results from a T to C substitution at nucleotide position 1508, causing the phenylalanine (F) at amino acid position 503 to be replaced by a serine (S). 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