rs7705189

Positions:

• chr5-132287665-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431054.5(P4HA2):​c.78+7513T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,060 control chromosomes in the GnomAD database, including 11,362 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 0.37 (11362 hom., cov: 32)
• Consequence: P4HA2 ENST00000431054.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

Genes affected

P4HA2 (HGNC:):

P4HA2 (HGNC:8547): (prolyl 4-hydroxylase subunit alpha 2) This gene encodes a component of prolyl 4-hydroxylase, a key enzyme in collagen synthesis composed of two identical alpha subunits and two beta subunits. The encoded protein is one of several different types of alpha subunits and provides the major part of the catalytic site of the active enzyme. In collagen and related proteins, prolyl 4-hydroxylase catalyzes the formation of 4-hydroxyproline that is essential to the proper three-dimensional folding of newly synthesized procollagen chains. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.132287665A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
P4HA2	ENST00000471826.1	n.139-6711T>C		intron_variant		1
P4HA2	ENST00000431054.5	c.78+7513T>C		intron_variant		4		ENSP00000391257.1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56228 AN: 151942 Hom.: 11360 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.420

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.370 AC: 56246 AN: 152060 Hom.: 11362 Cov.: 32 AF XY: 0.355 AC XY: 26396 AN XY: 74312

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.414

Alfa AF: 0.384 Hom.: 1814

Bravo AF: 0.378

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7705189; hg19: chr5-131623358;