1-15466137-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BS2_Supporting
The NM_033440.3(CELA2A):āc.632G>Cā(p.Ser211Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,846 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_033440.3 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 |
---|---|---|---|---|---|---|---|
CELA2A | NM_033440.3 | c.632G>C | p.Ser211Thr | missense_variant | 6/8 | ENST00000359621.5 | |
LOC105376767 | XR_002958256.2 | n.366+1003C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CELA2A | ENST00000359621.5 | c.632G>C | p.Ser211Thr | missense_variant | 6/8 | 1 | NM_033440.3 | P1 | |
CELA2B | ENST00000494280.1 | n.229G>C | non_coding_transcript_exon_variant | 1/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251278Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135800
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461576Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727030
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 08, 2024 | The c.632G>C (p.S211T) alteration is located in exon 6 (coding exon 6) of the CELA2A gene. This alteration results from a G to C substitution at nucleotide position 632, causing the serine (S) at amino acid position 211 to be replaced by a threonine (T). 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