dbSNP rs4826381: PAGE3:p.Asn35Asp (chrX-55263341-T-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001017931.3(PAGE3):c.103A>G(p.Asn35Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.84 ( 28884 hom., 27106 hem., cov: 22)

Exomes 𝑓: 0.95 ( 129890 hom. 162376 hem. )

Failed GnomAD Quality Control

Consequence

PAGE3
NM_001017931.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.122

Variant links:

Genes affected

PAGE3 (HGNC:4110): (PAGE family member 3) This gene is a member of family of proteins that are expressed in a variety of tumors and in some fetal and reproductive tissues. Multiple alternatively spliced transcript variants have been observed. [provided by RefSeq, Jan 2015]

PAGE3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.34829115E-5).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAGE3	NM_001017931.3 link	c.103A>G	p.Asn35Asp	missense_variant	Exon 3 of 5	ENST00000374951.6	NP_001017931.3	Q5JUK9
PAGE3	NM_001171252.2 link	c.103A>G	p.Asn35Asp	missense_variant	Exon 3 of 5		NP_001164723.2	Q5JUK9
PAGE3	NM_001303613.2 link	c.103A>G	p.Asn35Asp	missense_variant	Exon 3 of 5		NP_001290542.2	Q5JUK9
PAGE3	XM_017029282.3 link	c.103A>G	p.Asn35Asp	missense_variant	Exon 3 of 5		XP_016884771.1	Q5JUK9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAGE3	ENST00000374951.6 link	c.103A>G	p.Asn35Asp	missense_variant	Exon 3 of 5	1	NM_001017931.3	ENSP00000364089.1		Q5JUK9
PAGE3	ENST00000519203.1 link	c.103A>G	p.Asn35Asp	missense_variant	Exon 3 of 5	1		ENSP00000429571.1		Q5JUK9

Frequencies

GnomAD3 genomes

AF:

0.841

AC:

92285

AN:

109678

Hom.:

28891

Cov.:

AF XY:

0.847

AC XY:

27064

AN XY:

31952

show subpopulations

Gnomad AFR

AF:

0.523

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.922

Gnomad ASJ

AF:

0.930

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.926

Gnomad FIN

AF:

0.993

Gnomad MID

AF:

0.801

Gnomad NFE

AF:

0.970

Gnomad OTH

AF:

0.856

GnomAD3 exomes

AF:

0.934

AC:

169359

AN:

181367

Hom.:

50724

AF XY:

0.944

AC XY:

62158

AN XY:

65875

show subpopulations

Gnomad AFR exome

AF:

0.516

Gnomad AMR exome

AF:

0.962

Gnomad ASJ exome

AF:

0.924

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.930

Gnomad FIN exome

AF:

0.993

Gnomad NFE exome

AF:

0.969

Gnomad OTH exome

AF:

0.949

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.949

AC:

433792

AN:

456869

Hom.:

129890

Cov.:

AF XY:

0.951

AC XY:

162376

AN XY:

170659

show subpopulations

Gnomad4 AFR exome

AF:

0.521

Gnomad4 AMR exome

AF:

0.957

Gnomad4 ASJ exome

AF:

0.921

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.929

Gnomad4 FIN exome

AF:

0.992

Gnomad4 NFE exome

AF:

0.969

Gnomad4 OTH exome

AF:

0.923

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.841

AC:

92312

AN:

109735

Hom.:

28884

Cov.:

AF XY:

0.847

AC XY:

27106

AN XY:

32019

show subpopulations

Gnomad4 AFR

AF:

0.523

Gnomad4 AMR

AF:

0.922

Gnomad4 ASJ

AF:

0.930

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.926

Gnomad4 FIN

AF:

0.993

Gnomad4 NFE

AF:

0.970

Gnomad4 OTH

AF:

0.858

Alfa

AF:

0.932

Hom.:

60979

Bravo

AF:

0.824

TwinsUK

AF:

0.978

AC:

3628

ALSPAC

AF:

0.979

AC:

2828

ESP6500AA

AF:

0.531

AC:

2036

ESP6500EA

AF:

0.968

AC:

6514

ExAC

AF:

0.926

AC:

112375

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.051

BayesDel_addAF

Benign

-1.1

BayesDel_noAF

Benign

-1.2

CADD

Benign

0.19

DANN

Benign

0.15

DEOGEN2

Benign

0.0010

T;T

FATHMM_MKL

Benign

0.00011

LIST_S2

Benign

0.18

.;T

MetaRNN

Benign

0.000013

T;T

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.36

PROVEAN

Benign

1.8

N;N

REVEL

Benign

0.012

Sift

Benign

0.98

T;T

Sift4G

Benign

0.81

T;T

Polyphen

0.0

B;B

Vest4

0.036

MPC

0.0049

ClinPred

0.000016

GERP RS

1.1

Varity_R

0.056

gMVP

0.0055

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over