rs1393901
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000297770.10(CPA6):c.318-1444A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,994 control chromosomes in the GnomAD database, including 17,300 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.46 ( 17300 hom., cov: 32)
Consequence
CPA6
ENST00000297770.10 intron
ENST00000297770.10 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0630
Genes affected
CPA6 (HGNC:17245): (carboxypeptidase A6) The gene encodes a member of the peptidase M14 family of metallocarboxypeptidases. The encoded preproprotein is proteolytically processed to generate the mature enzyme, which catalyzes the release of large hydrophobic C-terminal amino acids. This enzyme has functions ranging from digestion of food to selective biosynthesis of neuroendocrine peptides. Mutations in this gene may be linked to epilepsy and febrile seizures, and a translocation t(6;8)(q26;q13) involving this gene has been associated with Duane retraction syndrome. [provided by RefSeq, May 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPA6 | NM_020361.5 | c.318-1444A>G | intron_variant | ENST00000297770.10 | NP_065094.3 | |||
CPA6 | XM_017013646.2 | c.-127-1444A>G | intron_variant | XP_016869135.1 | ||||
CPA6 | XM_017013647.2 | c.318-1444A>G | intron_variant | XP_016869136.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPA6 | ENST00000297770.10 | c.318-1444A>G | intron_variant | 1 | NM_020361.5 | ENSP00000297770 | P1 | |||
CPA6 | ENST00000479862.6 | c.193-1444A>G | intron_variant, NMD_transcript_variant | 1 | ENSP00000419016 | |||||
CPA6 | ENST00000518549.1 | n.532-1444A>G | intron_variant, non_coding_transcript_variant | 1 | ||||||
CPA6 | ENST00000638254.1 | c.193-1444A>G | intron_variant, NMD_transcript_variant | 5 | ENSP00000491129 |
Frequencies
GnomAD3 genomes AF: 0.456 AC: 69235AN: 151876Hom.: 17270 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.456 AC: 69306AN: 151994Hom.: 17300 Cov.: 32 AF XY: 0.452 AC XY: 33563AN XY: 74304
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1167
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3478
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at