14-74955472-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002632.6(PGF):c.-230G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 388,668 control chromosomes in the GnomAD database, including 172 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 0.023 ( 146 hom., cov: 32)
Exomes 𝑓: 0.0029 ( 26 hom. )
Consequence
PGF
NM_002632.6 5_prime_UTR
NM_002632.6 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.255
Genes affected
PGF (HGNC:8893): (placental growth factor) Enables growth factor activity. Involved in positive regulation of cell population proliferation. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Implicated in several diseases, including brain ischemia; diabetic neuropathy; glioblastoma; myocardial infarction; and pancreatic endocrine carcinoma. Biomarker of several diseases, including artery disease (multiple); autoimmune disease of musculoskeletal system (multiple); epilepsy (multiple); limited scleroderma; and pancreatic endocrine carcinoma. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.69).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0768 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGF | NM_002632.6 | c.-230G>A | 5_prime_UTR_variant | 1/7 | ENST00000555567.6 | ||
PGF | NM_001207012.1 | c.-230G>A | 5_prime_UTR_variant | 1/6 | |||
PGF | NM_001293643.1 | c.-230G>A | 5_prime_UTR_variant | 1/7 | |||
PGF | XM_047431476.1 | c.-230G>A | 5_prime_UTR_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGF | ENST00000555567.6 | c.-230G>A | 5_prime_UTR_variant | 1/7 | 1 | NM_002632.6 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0227 AC: 3449AN: 152096Hom.: 146 Cov.: 32
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GnomAD4 exome AF: 0.00292 AC: 690AN: 236458Hom.: 26 Cov.: 0 AF XY: 0.00242 AC XY: 292AN XY: 120428
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GnomAD4 genome AF: 0.0227 AC: 3454AN: 152210Hom.: 146 Cov.: 32 AF XY: 0.0210 AC XY: 1560AN XY: 74408
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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