Variant chr7-101206172-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001084.5(PLOD3):c.*109T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00923 in 1,129,430 control chromosomes in the GnomAD database, including 203 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.013 ( 38 hom., cov: 32)

Exomes 𝑓: 0.0086 ( 165 hom. )

Consequence

PLOD3
NM_001084.5 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.107

Variant links:

Genes affected

PLOD3 (HGNC:9083): (procollagen-lysine,2-oxoglutarate 5-dioxygenase 3) The protein encoded by this gene is a membrane-bound homodimeric enzyme that is localized to the cisternae of the rough endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in collagen-like peptides. The resultant hydroxylysyl groups are attachment sites for carbohydrates in collagen and thus are critical for the stability of intermolecular crosslinks. Some patients with Ehlers-Danlos syndrome type VIB have deficiencies in lysyl hydroxylase activity. [provided by RefSeq, Jul 2008]

PLOD3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 7-101206172-A-C is Benign according to our data. Variant chr7-101206172-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2663317.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLOD3	NM_001084.5 linkuse as main transcript	c.*109T>G		3_prime_UTR_variant	19/19	ENST00000223127.8	NP_001075.1	O60568Q9UG85

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLOD3	ENST00000223127 linkuse as main transcript	c.*109T>G		3_prime_UTR_variant	19/19	1	NM_001084.5	ENSP00000223127.3		O60568
PLOD3	ENST00000454310 linkuse as main transcript	c.*109T>G		3_prime_UTR_variant	7/7	5		ENSP00000407555.1		H7C2S8

Frequencies

GnomAD3 genomes

AF:

0.0130

AC:

1972

AN:

152098

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0239

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0108

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.0861

Gnomad SAS

AF:

0.0174

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00387

Gnomad OTH

AF:

0.00862

GnomAD4 exome

AF:

0.00863

AC:

8429

AN:

977214

Hom.:

165

Cov.:

AF XY:

0.00896

AC XY:

4544

AN XY:

506874

show subpopulations

Gnomad4 AFR exome

AF:

0.0225

Gnomad4 AMR exome

AF:

0.00446

Gnomad4 ASJ exome

AF:

0.000823

Gnomad4 EAS exome

AF:

0.0783

Gnomad4 SAS exome

AF:

0.0173

Gnomad4 FIN exome

AF:

0.000215

Gnomad4 NFE exome

AF:

0.00424

Gnomad4 OTH exome

AF:

0.0119

GnomAD4 genome

AF:

0.0131

AC:

1990

AN:

152216

Hom.:

Cov.:

AF XY:

0.0132

AC XY:

981

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0242

Gnomad4 AMR

AF:

0.0108

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.0863

Gnomad4 SAS

AF:

0.0176

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00387

Gnomad4 OTH

AF:

0.00853

Alfa

AF:

0.000844

Hom.:

Bravo

AF:

0.0146

Asia WGS

AF:

0.0700

AC:

243

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

May 22, 2021

See Variant Classification Assertion Criteria. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.2

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over