Variant rs1800897 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000278.5(PAX2):c.798C>T(p.Asn266Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0584 in 1,611,838 control chromosomes in the GnomAD database, including 6,422 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 2438 hom., cov: 32)

Exomes 𝑓: 0.051 ( 3984 hom. )

Consequence

PAX2
NM_000278.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7O:1

Conservation

PhyloP100: -0.215

Variant links:

Genes affected

PAX2 (HGNC:8616): (paired box 2) PAX2 encodes paired box gene 2, one of many human homologues of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcriptional supression by the tumor suppressor gene WT1. Mutations within PAX2 have been shown to result in optic nerve colobomas and renal hypoplasia. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2014]

PAX2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 10-100809115-C-T is Benign according to our data. Variant chr10-100809115-C-T is described in ClinVar as [Benign]. Clinvar id is 156298.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-100809115-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.215 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAX2	NM_000278.5 link	c.798C>T	p.Asn266Asn	synonymous_variant	7/10	ENST00000355243.8	NP_000269.3	Q02962-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PAX2	ENST00000355243.8 link	c.798C>T	p.Asn266Asn	synonymous_variant	7/10	1	NM_000278.5	ENSP00000347385.3		Q02962-3

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18930

AN:

151972

Hom.:

2432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.124

Gnomad AMR

AF:

0.0694

Gnomad ASJ

AF:

0.0248

Gnomad EAS

AF:

0.0905

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.0273

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0381

Gnomad OTH

AF:

0.0951

GnomAD3 exomes

AF:

0.0744

AC:

18703

AN:

251364

Hom.:

1442

AF XY:

0.0706

AC XY:

9587

AN XY:

135864

show subpopulations

Gnomad AFR exome

AF:

0.334

Gnomad AMR exome

AF:

0.0697

Gnomad ASJ exome

AF:

0.0217

Gnomad EAS exome

AF:

0.0975

Gnomad SAS exome

AF:

0.112

Gnomad FIN exome

AF:

0.0269

Gnomad NFE exome

AF:

0.0397

Gnomad OTH exome

AF:

0.0534

GnomAD4 exome

AF:

0.0515

AC:

75169

AN:

1459748

Hom.:

3984

Cov.:

AF XY:

0.0522

AC XY:

37890

AN XY:

726358

show subpopulations

Gnomad4 AFR exome

AF:

0.346

Gnomad4 AMR exome

AF:

0.0667

Gnomad4 ASJ exome

AF:

0.0227

Gnomad4 EAS exome

AF:

0.0993

Gnomad4 SAS exome

AF:

0.110

Gnomad4 FIN exome

AF:

0.0254

Gnomad4 NFE exome

AF:

0.0367

Gnomad4 OTH exome

AF:

0.0671

GnomAD4 genome

AF:

0.125

AC:

18975

AN:

152090

Hom.:

2438

Cov.:

AF XY:

0.124

AC XY:

9200

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.329

Gnomad4 AMR

AF:

0.0694

Gnomad4 ASJ

AF:

0.0248

Gnomad4 EAS

AF:

0.0903

Gnomad4 SAS

AF:

0.108

Gnomad4 FIN

AF:

0.0273

Gnomad4 NFE

AF:

0.0381

Gnomad4 OTH

AF:

0.0989

Alfa

AF:

0.0617

Hom.:

974

Bravo

AF:

0.137

Asia WGS

AF:

0.146

AC:

510

AN:

3478

EpiCase

AF:

0.0412

EpiControl

AF:

0.0372

ClinVar

Significance: Benign

Submissions summary: Benign:7Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

not provided

Benign:2Other:1

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
not provided, no classification provided	literature only	ClinVar Staff, National Center for Biotechnology Information (NCBI)	-	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Renal coloboma syndrome;C4014925:Focal segmental glomerulosclerosis 7

Benign:2

Benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Dec 29, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

1.1

DANN

Benign

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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