rs7078127

Positions:

• chr10-73087876-A-C

Variant summary

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

The NM_001017962.3(P4HA1):​c.-33+8890T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,096 control chromosomes in the GnomAD database, including 1,267 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 0.11 (1267 hom., cov: 32)
• Consequence: P4HA1 NM_001017962.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

Genes affected

P4HA1 (HGNC:8546): (prolyl 4-hydroxylase subunit alpha 1) 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
P4HA1	NM_001017962.3	c.-33+8890T>G		intron_variant		ENST00000394890.7	NP_001017962.1
P4HA1	NM_000917.4	c.-33+8890T>G		intron_variant			NP_000908.2
P4HA1	NM_001142595.2	c.-126+8890T>G		intron_variant			NP_001136067.1
P4HA1	NM_001142596.2	c.-33+8890T>G		intron_variant			NP_001136068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
P4HA1	ENST00000394890.7	c.-33+8890T>G		intron_variant		1	NM_001017962.3	ENSP00000378353	A1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16305 AN: 151978 Hom.: 1248 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.108 AC: 16357 AN: 152096 Hom.: 1267 Cov.: 32 AF XY: 0.110 AC XY: 8145 AN XY: 74360

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0894

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.0412

Gnomad4 NFE AF: 0.0610

Gnomad4 OTH AF: 0.0972

Alfa AF: 0.0854 Hom.: 127

Bravo AF: 0.111

Asia WGS AF: 0.251 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.3
DANN	Benign	0.68

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: rs7078127; hg19: chr10-74847634;