5-132233934-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000431054.5(P4HA2):c.79-15290A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,128 control chromosomes in the GnomAD database, including 26,323 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 0.58 ( 26323 hom., cov: 33)
Consequence
P4HA2
ENST00000431054.5 intron
ENST00000431054.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.274
Publications
18 publications found
Genes affected
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]
P4HA2 Gene-Disease associations (from GenCC):
- myopiaInheritance: AD Classification: STRONG Submitted by: G2P
- myopia 25, autosomal dominantInheritance: Unknown, AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
P4HA2 | ENST00000431054.5 | c.79-15290A>G | intron_variant | Intron 1 of 5 | 4 | ENSP00000391257.1 | ||||
P4HA2 | ENST00000439698.5 | c.-18-15290A>G | intron_variant | Intron 2 of 6 | 5 | ENSP00000405406.1 | ||||
P4HA2 | ENST00000416053.5 | c.-18-15290A>G | intron_variant | Intron 1 of 3 | 3 | ENSP00000394953.1 |
Frequencies
GnomAD3 genomes AF: 0.583 AC: 88666AN: 152010Hom.: 26304 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
88666
AN:
152010
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.583 AC: 88723AN: 152128Hom.: 26323 Cov.: 33 AF XY: 0.571 AC XY: 42437AN XY: 74378 show subpopulations
GnomAD4 genome
AF:
AC:
88723
AN:
152128
Hom.:
Cov.:
33
AF XY:
AC XY:
42437
AN XY:
74378
show subpopulations
African (AFR)
AF:
AC:
23506
AN:
41496
American (AMR)
AF:
AC:
8262
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
2161
AN:
3468
East Asian (EAS)
AF:
AC:
2709
AN:
5172
South Asian (SAS)
AF:
AC:
1750
AN:
4818
European-Finnish (FIN)
AF:
AC:
5053
AN:
10586
Middle Eastern (MID)
AF:
AC:
166
AN:
292
European-Non Finnish (NFE)
AF:
AC:
43044
AN:
67984
Other (OTH)
AF:
AC:
1251
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1899
3797
5696
7594
9493
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
744
1488
2232
2976
3720
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1574
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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