chr1-15466145-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_033440.3(CELA2A):c.639+1G>C variant causes a splice donor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,270 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_033440.3 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CELA2A | NM_033440.3 | c.639+1G>C | splice_donor_variant | ENST00000359621.5 | |||
LOC105376767 | XR_002958256.2 | n.366+995C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CELA2A | ENST00000359621.5 | c.639+1G>C | splice_donor_variant | 1 | NM_033440.3 | P1 | |||
CELA2B | ENST00000494280.1 | n.236+1G>C | splice_donor_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461270Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726812
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hypertensive disorder;C0813230:Hypertriglyceridemia;C1320657:Diabetes;C1956346:Coronary artery disorder Pathogenic:1
Pathogenic, no assertion criteria provided | research | Mani Lab, Yale Cardiovascular Research Center, Yale University | Jan 01, 2017 | - - |
Abdominal obesity-metabolic syndrome 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 11, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at