NM_001079807.4:c.867C>T
Variant names:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001079807.4(PGA3):c.867C>T(p.Pro289Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0046 ( 0 hom., cov: 7)
Exomes 𝑓: 0.0063 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
PGA3
NM_001079807.4 synonymous
NM_001079807.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.329
Genes affected
PGA3 (HGNC:8885): (pepsinogen A3) This gene encodes a protein precursor of the digestive enzyme pepsin, a member of the peptidase A1 family of endopeptidases. The encoded precursor is secreted by gastric chief cells and undergoes autocatalytic cleavage in acidic conditions to form the active enzyme, which functions in the digestion of dietary proteins. This gene is found in a cluster of related genes on chromosome 11, each of which encodes one of multiple pepsinogens. Pepsinogen levels in serum may serve as a biomarker for atrophic gastritis and gastric cancer. [provided by RefSeq, Jul 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 11-61211183-C-T is Benign according to our data. Variant chr11-61211183-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3777979.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.329 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00456 AC: 281AN: 61630Hom.: 0 Cov.: 7
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GnomAD3 exomes AF: 0.00521 AC: 315AN: 60404Hom.: 0 AF XY: 0.00545 AC XY: 167AN XY: 30656
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00626 AC: 2760AN: 440628Hom.: 1 Cov.: 4 AF XY: 0.00603 AC XY: 1391AN XY: 230626
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00456 AC: 281AN: 61652Hom.: 0 Cov.: 7 AF XY: 0.00453 AC XY: 128AN XY: 28278
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
PGA3: BP4, BP7 -
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
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