1-15466127-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBS2_Supporting
The NM_033440.3(CELA2A):c.622G>A(p.Val208Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,814 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 (★).
Frequency
Consequence
NM_033440.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CELA2A | NM_033440.3 | c.622G>A | p.Val208Met | missense_variant | 6/8 | ENST00000359621.5 | |
LOC105376767 | XR_002958256.2 | n.366+1013C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CELA2A | ENST00000359621.5 | c.622G>A | p.Val208Met | missense_variant | 6/8 | 1 | NM_033440.3 | P1 | |
CELA2B | ENST00000494280.1 | n.219G>A | non_coding_transcript_exon_variant | 1/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251316Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135822
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461680Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727120
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2024 | The c.622G>A (p.V208M) alteration is located in exon 6 (coding exon 6) of the CELA2A gene. This alteration results from a G to A substitution at nucleotide position 622, causing the valine (V) at amino acid position 208 to be replaced by a methionine (M). 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