chr7-130380529-G-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001868.4(CPA1):c.9G>T(p.Gly3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000516 in 1,163,290 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G3G) has been classified as Likely benign.
Frequency
Consequence
NM_001868.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPA1 | NM_001868.4 | c.9G>T | p.Gly3= | synonymous_variant | 1/10 | ENST00000011292.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPA1 | ENST00000011292.8 | c.9G>T | p.Gly3= | synonymous_variant | 1/10 | 1 | NM_001868.4 | P1 | |
CPA1 | ENST00000604896.5 | c.9G>T | p.Gly3= | synonymous_variant | 1/6 | 3 | |||
CPA1 | ENST00000481342.5 | c.-200+120G>T | intron_variant | 3 | |||||
CPA1 | ENST00000491460.5 | n.36G>T | non_coding_transcript_exon_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000827 AC: 1AN: 120860Hom.: 0 AF XY: 0.0000155 AC XY: 1AN XY: 64594
GnomAD4 exome AF: 0.00000516 AC: 6AN: 1163290Hom.: 0 Cov.: 29 AF XY: 0.00000538 AC XY: 3AN XY: 557380
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Hereditary pancreatitis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at