3-189963671-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_018192.4(P3H2):c.2034+287G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00905 in 388,160 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 38 hom., cov: 32)
Exomes 𝑓: 0.0053 ( 29 hom. )
Consequence
P3H2
NM_018192.4 intron
NM_018192.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.794
Genes affected
P3H2 (HGNC:19317): (prolyl 3-hydroxylase 2) This gene encodes a member of the prolyl 3-hydroxylase subfamily of 2-oxo-glutarate-dependent dioxygenases. These enzymes play a critical role in collagen chain assembly, stability and cross-linking by catalyzing post-translational 3-hydroxylation of proline residues. Mutations in this gene are associated with nonsyndromic severe myopia with cataract and vitreoretinal degeneration, and downregulation of this gene may play a role in breast cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
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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=-1.03).
BP6
?
Variant 3-189963671-C-T is Benign according to our data. Variant chr3-189963671-C-T is described in ClinVar as [Benign]. Clinvar id is 1235572.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0149 (2267/152130) while in subpopulation AFR AF= 0.0482 (1998/41492). AF 95% confidence interval is 0.0464. There are 38 homozygotes in gnomad4. There are 1086 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 38 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P3H2 | NM_018192.4 | c.2034+287G>A | intron_variant | ENST00000319332.10 | |||
P3H2 | NM_001134418.2 | c.1491+287G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P3H2 | ENST00000319332.10 | c.2034+287G>A | intron_variant | 1 | NM_018192.4 | P1 | |||
P3H2 | ENST00000427335.6 | c.1491+287G>A | intron_variant | 1 | |||||
P3H2 | ENST00000463171.5 | n.542G>A | non_coding_transcript_exon_variant | 3/3 | 5 | ||||
P3H2 | ENST00000490940.1 | n.164+287G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0149 AC: 2266AN: 152012Hom.: 38 Cov.: 32
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GnomAD4 exome AF: 0.00528 AC: 1246AN: 236030Hom.: 29 Cov.: 0 AF XY: 0.00626 AC XY: 781AN XY: 124800
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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 | GeneDx | Feb 14, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at