chr19-16896339-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_015692.5(CPAMD8):c.5276-13C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,595,808 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0055 ( 13 hom., cov: 31)
Exomes 𝑓: 0.00054 ( 9 hom. )
Consequence
CPAMD8
NM_015692.5 splice_polypyrimidine_tract, intron
NM_015692.5 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.649
Genes affected
CPAMD8 (HGNC:23228): (C3 and PZP like alpha-2-macroglobulin domain containing 8) This gene encodes a member of the protease inhibitor I39 (alpha-2-macroglobulin) family of proteins. These proteins are important in innate and acquired immunity. The encoded protein is membrane-associated and proteolytically processed to generate two chains. Mutations in this gene cause a form of anterior segment dysgenesis, a developmental disorder of the eye. [provided by RefSeq, May 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 19-16896339-G-A is Benign according to our data. Variant chr19-16896339-G-A is described in ClinVar as [Benign]. Clinvar id is 3020555.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00547 (833/152232) while in subpopulation AFR AF= 0.0193 (801/41550). AF 95% confidence interval is 0.0182. There are 13 homozygotes in gnomad4. There are 364 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPAMD8 | NM_015692.5 | c.5276-13C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000443236.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPAMD8 | ENST00000443236.7 | c.5276-13C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015692.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00546 AC: 830AN: 152116Hom.: 13 Cov.: 31
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GnomAD3 exomes AF: 0.00113 AC: 242AN: 214824Hom.: 3 AF XY: 0.000780 AC XY: 92AN XY: 117892
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GnomAD4 exome AF: 0.000539 AC: 778AN: 1443576Hom.: 9 Cov.: 32 AF XY: 0.000444 AC XY: 318AN XY: 716530
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GnomAD4 genome AF: 0.00547 AC: 833AN: 152232Hom.: 13 Cov.: 31 AF XY: 0.00489 AC XY: 364AN XY: 74444
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 13, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at