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GeneBe

rs7078127

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.217
Variant links:
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]

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ACMG classification

Classification made for transcript

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 UniProt
P4HA1NM_001017962.3 linkuse as main transcriptc.-33+8890T>G intron_variant ENST00000394890.7
P4HA1NM_000917.4 linkuse as main transcriptc.-33+8890T>G intron_variant
P4HA1NM_001142595.2 linkuse as main transcriptc.-126+8890T>G intron_variant
P4HA1NM_001142596.2 linkuse as main transcriptc.-33+8890T>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
P4HA1ENST00000394890.7 linkuse as main transcriptc.-33+8890T>G intron_variant 1 NM_001017962.3 A1P13674-1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7078127; hg19: chr10-74847634; API