1-42762312-GTT-GTTTT

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The ENST00000492956.1(P3H1):n.673_674dupAA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000404 in 1,610,386 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000042 ( 0 hom. )

Consequence

P3H1
ENST00000492956.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.435

Publications

0 publications found

Variant links:

Genes affected

P3H1 (HGNC:19316): (prolyl 3-hydroxylase 1) This gene encodes an enzyme that is a member of the collagen prolyl hydroxylase family. These enzymes are localized to the endoplasmic reticulum and their activity is required for proper collagen synthesis and assembly. Mutations in this gene are associated with osteogenesis imperfecta type VIII. Three alternatively spliced transcript variants encoding different isoforms have been described. Other variants may exist, but their biological validity has not been determined. [provided by RefSeq, Aug 2011]

P3H1 Gene-Disease associations (from GenCC):

osteogenesis imperfecta type 8
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
osteogenesis imperfecta type 2
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
osteogenesis imperfecta type 3
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

P3H1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP6

Variant 1-42762312-G-GTT is Benign according to our data. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42762312-G-GTT is described in CliVar as Benign. Clinvar id is 1673011.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
P3H1	NM_022356.4 link	c.618+9_618+10dupAA		intron_variant	Intron 2 of 14	ENST00000296388.10	NP_071751.3	Q32P28-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
P3H1	ENST00000296388.10 link	c.618+9_618+10dupAA		intron_variant	Intron 2 of 14	1	NM_022356.4	ENSP00000296388.5		Q32P28-1

Frequencies

GnomAD3 genomes

AF:

0.0000264

AC:

AN:

151694

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000589

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000318

AC:

AN:

251472

AF XY:

0.0000294

show subpopulations

Gnomad AFR exome

AF:

0.0000615

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000527

Gnomad OTH exome

AF:

0.000163

GnomAD4 exome

AF:

0.0000418

AC:

AN:

1458692

Hom.:

Cov.:

AF XY:

0.0000413

AC XY:

AN XY:

725848

show subpopulations

African (AFR)

AF:

0.0000299

AC:

AN:

33406

American (AMR)

AF:

0.00

AC:

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26100

East Asian (EAS)

AF:

0.00

AC:

AN:

39664

South Asian (SAS)

AF:

0.00

AC:

AN:

86206

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53360

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5762

European-Non Finnish (NFE)

AF:

0.0000541

AC:

AN:

1109218

Other (OTH)

AF:

0.00

AC:

AN:

60264

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000264

AC:

AN:

151694

Hom.:

Cov.:

AF XY:

0.0000405

AC XY:

AN XY:

74102

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41266

American (AMR)

AF:

0.00

AC:

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5178

South Asian (SAS)

AF:

0.00

AC:

AN:

4802

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10536

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000589

AC:

AN:

67910

Other (OTH)

AF:

0.00

AC:

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.538

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.0000434

Hom.:

Bravo

AF:

0.0000340

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Osteogenesis imperfecta type 8

Benign:1

Oct 18, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.43

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over