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GeneBe

3-157436979-T-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_002852.4(PTX3):c.46T>C(p.Leu16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0111 in 1,614,060 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0095 ( 9 hom., cov: 32)
Exomes 𝑓: 0.011 ( 88 hom. )

Consequence

PTX3
NM_002852.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.164
Variant links:
Genes affected
PTX3 (HGNC:9692): (pentraxin 3) This gene encodes a member of the pentraxin protein family. The expression of this protein is induced by inflammatory cytokines in response to inflammatory stimuli in several mesenchymal and epithelial cell types, particularly endothelial cells and mononuclear phagocytes. The protein promotes fibrocyte differentiation and is involved in regulating inflammation and complement activation. It also plays a role in angiogenesis and tissue remodeling. The protein serves as a biomarker for several inflammatory conditions. [provided by RefSeq, Jun 2016]
VEPH1 (HGNC:25735): (ventricular zone expressed PH domain containing 1) Predicted to enable phosphatidylinositol-5-phosphate binding activity. Involved in negative regulation of SMAD protein signal transduction and negative regulation of transforming growth factor beta receptor signaling pathway. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-157436979-T-C is Benign according to our data. Variant chr3-157436979-T-C is described in ClinVar as [Benign]. Clinvar id is 770537.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.164 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 9 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTX3NM_002852.4 linkuse as main transcriptc.46T>C p.Leu16= synonymous_variant 1/3 ENST00000295927.4
VEPH1NM_001167912.2 linkuse as main transcriptc.530-8491A>G intron_variant ENST00000362010.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTX3ENST00000295927.4 linkuse as main transcriptc.46T>C p.Leu16= synonymous_variant 1/31 NM_002852.4 P1
VEPH1ENST00000362010.7 linkuse as main transcriptc.530-8491A>G intron_variant 1 NM_001167912.2 P1Q14D04-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00950
AC:
1446
AN:
152212
Hom.:
9
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00239
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.00948
Gnomad ASJ
AF:
0.00806
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00104
Gnomad FIN
AF:
0.0154
Gnomad MID
AF:
0.00637
Gnomad NFE
AF:
0.0142
Gnomad OTH
AF:
0.0158
GnomAD3 exomes
AF:
0.00905
AC:
2275
AN:
251424
Hom.:
16
AF XY:
0.00904
AC XY:
1229
AN XY:
135892
show subpopulations
Gnomad AFR exome
AF:
0.00209
Gnomad AMR exome
AF:
0.00802
Gnomad ASJ exome
AF:
0.00804
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.00124
Gnomad FIN exome
AF:
0.0140
Gnomad NFE exome
AF:
0.0130
Gnomad OTH exome
AF:
0.0106
GnomAD4 exome
AF:
0.0112
AC:
16394
AN:
1461730
Hom.:
88
Cov.:
30
AF XY:
0.0109
AC XY:
7906
AN XY:
727178
show subpopulations
Gnomad4 AFR exome
AF:
0.00170
Gnomad4 AMR exome
AF:
0.00805
Gnomad4 ASJ exome
AF:
0.00784
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.00108
Gnomad4 FIN exome
AF:
0.0144
Gnomad4 NFE exome
AF:
0.0129
Gnomad4 OTH exome
AF:
0.00931
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00949
AC:
1445
AN:
152330
Hom.:
9
Cov.:
32
AF XY:
0.00959
AC XY:
714
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.00238
Gnomad4 AMR
AF:
0.00947
Gnomad4 ASJ
AF:
0.00806
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00104
Gnomad4 FIN
AF:
0.0154
Gnomad4 NFE
AF:
0.0142
Gnomad4 OTH
AF:
0.0156
Alfa
AF:
0.0122
Hom.:
6
Bravo
AF:
0.00863
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.0104
EpiControl
AF:
0.0112

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 19, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
Cadd
Benign
6.8
Dann
Benign
0.75

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: rs35948036; hg19: chr3-157154768; COSMIC: COSV55822494; COSMIC: COSV55822494; API