chr3-189957700-A-AAGAGAGAGAG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_018192.4(P3H2):c.*211_*212insCTCTCTCTCT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.016 ( 24 hom., cov: 0)
Exomes 𝑓: 0.010 ( 5 hom. )
Consequence
P3H2
NM_018192.4 3_prime_UTR
NM_018192.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.38
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 -10 ACMG points.
BP6
?
Variant 3-189957700-A-AAGAGAGAGAG is Benign according to our data. Variant chr3-189957700-A-AAGAGAGAGAG is described in ClinVar as [Likely_benign]. Clinvar id is 1195289.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0164 (2413/147564) while in subpopulation AFR AF= 0.0257 (1031/40124). AF 95% confidence interval is 0.0244. There are 24 homozygotes in gnomad4. There are 1159 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 24 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
P3H2 | NM_018192.4 | c.*211_*212insCTCTCTCTCT | 3_prime_UTR_variant | 15/15 | ENST00000319332.10 | ||
P3H2 | NM_001134418.2 | c.*211_*212insCTCTCTCTCT | 3_prime_UTR_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
P3H2 | ENST00000319332.10 | c.*211_*212insCTCTCTCTCT | 3_prime_UTR_variant | 15/15 | 1 | NM_018192.4 | P1 | ||
P3H2 | ENST00000427335.6 | c.*211_*212insCTCTCTCTCT | 3_prime_UTR_variant | 15/15 | 1 | ||||
P3H2 | ENST00000490940.1 | n.468_469insCTCTCTCTCT | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0163 AC: 2410AN: 147454Hom.: 24 Cov.: 0
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GnomAD4 exome AF: 0.0103 AC: 4065AN: 395278Hom.: 5 Cov.: 0 AF XY: 0.00987 AC XY: 2095AN XY: 212352
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GnomAD4 genome ? AF: 0.0164 AC: 2413AN: 147564Hom.: 24 Cov.: 0 AF XY: 0.0162 AC XY: 1159AN XY: 71684
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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
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 06, 2020 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at