3-189957700-A-AAGAGAGAGAG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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]

ACMG classification

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: 2410 AN: 147454 Hom.: 24 Cov.: 0

Gnomad AFR AF: 0.0257

Gnomad AMI AF: 0.00116

Gnomad AMR AF: 0.0189

Gnomad ASJ AF: 0.0319

Gnomad EAS AF: 0.00181

Gnomad SAS AF: 0.00683

Gnomad FIN AF: 0.00256

Gnomad MID AF: 0.0162

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0198

GnomAD4 exome AF: 0.0103 AC: 4065 AN: 395278 Hom.: 5 Cov.: 0 AF XY: 0.00987 AC XY: 2095 AN XY: 212352

Gnomad4 AFR exome AF: 0.0203

Gnomad4 AMR exome AF: 0.0152

Gnomad4 ASJ exome AF: 0.0245

Gnomad4 EAS exome AF: 0.00112

Gnomad4 SAS exome AF: 0.00487

Gnomad4 FIN exome AF: 0.00333

Gnomad4 NFE exome AF: 0.0112

Gnomad4 OTH exome AF: 0.0129

GnomAD4 genome AF: 0.0164 AC: 2413 AN: 147564 Hom.: 24 Cov.: 0 AF XY: 0.0162 AC XY: 1159 AN XY: 71684

Gnomad4 AFR AF: 0.0257

Gnomad4 AMR AF: 0.0188

Gnomad4 ASJ AF: 0.0319

Gnomad4 EAS AF: 0.00182

Gnomad4 SAS AF: 0.00706

Gnomad4 FIN AF: 0.00256

Gnomad4 NFE AF: 0.0132

Gnomad4 OTH AF: 0.0191

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 06, 2020

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3062112; hg19: chr3-189675489;