3-189963769-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_018192.4(P3H2):c.2034+189G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 663,260 control chromosomes in the GnomAD database, including 18,931 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.22 (3748 hom., cov: 32)
  • Exomes 𝑓: 0.24 (15183 hom.)
• Consequence: P3H2 NM_018192.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.45

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 3-189963769-C-G is Benign according to our data. Variant chr3-189963769-C-G is described in ClinVar as [Benign]. Clinvar id is 1241801.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
P3H2	NM_018192.4	c.2034+189G>C		intron_variant		ENST00000319332.10
P3H2	NM_001134418.2	c.1491+189G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
P3H2	ENST00000319332.10	c.2034+189G>C		intron_variant		1	NM_018192.4	P1
P3H2	ENST00000427335.6	c.1491+189G>C		intron_variant		1
P3H2	ENST00000463171.5	n.444G>C		non_coding_transcript_exon_variant	3/3	5
P3H2	ENST00000490940.1	n.164+189G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32708 AN: 151978 Hom.: 3742 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.240 AC: 122544 AN: 511164 Hom.: 15183 Cov.: 6 AF XY: 0.240 AC XY: 65332 AN XY: 271908

Gnomad4 AFR exome AF: 0.135

Gnomad4 AMR exome AF: 0.137

Gnomad4 ASJ exome AF: 0.247

Gnomad4 EAS exome AF: 0.171

Gnomad4 SAS exome AF: 0.219

Gnomad4 FIN exome AF: 0.217

Gnomad4 NFE exome AF: 0.267

Gnomad4 OTH exome AF: 0.232

GnomAD4 genome AF: 0.215 AC: 32733 AN: 152096 Hom.: 3748 Cov.: 32 AF XY: 0.211 AC XY: 15681 AN XY: 74344

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.210

Alfa AF: 0.138 Hom.: 252

Bravo AF: 0.206

Asia WGS AF: 0.186 AC: 652 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 28, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.55
Dann	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1719581; hg19: chr3-189681558; COSMIC: COSV60018095; COSMIC: COSV60018095;