7-127614497-G-A

Position:

chr7-127614497-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001366110.1(PAX4):c.421C>T(p.Arg141Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0053 in 1,595,834 control chromosomes in the GnomAD database, including 298 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 161 hom., cov: 32)

Exomes 𝑓: 0.0033 ( 137 hom. )

Consequence

PAX4
NM_001366110.1 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.67

Variant links:

Genes affected

PAX4 (HGNC:8618): (paired box 4) This gene is a member of the paired box (PAX) family of transcription factors. Members of this gene family typically contain a paired box domain, an octapeptide, and a paired-type homeodomain. These genes play critical roles during fetal development and cancer growth. The paired box 4 gene is involved in pancreatic islet development and mouse studies have demonstrated a role for this gene in differentiation of insulin-producing beta cells. [provided by RefSeq, Jul 2008]

PAX4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0025364459).

BP6

Variant 7-127614497-G-A is Benign according to our data. Variant chr7-127614497-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 13791.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAX4	NM_001366110.1 linkuse as main transcript	c.421C>T	p.Arg141Trp	missense_variant	6/12	ENST00000639438.3
PAX4	NM_001366111.1 linkuse as main transcript	c.421C>T	p.Arg141Trp	missense_variant	4/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAX4	ENST00000639438.3 linkuse as main transcript	c.421C>T	p.Arg141Trp	missense_variant	6/12	5	NM_001366110.1	A2

Frequencies

GnomAD3 genomes

AF:

0.0244

AC:

3711

AN:

152082

Hom.:

161

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0829

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0103

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000985

Gnomad OTH

AF:

0.0201

GnomAD3 exomes

AF:

0.00700

AC:

1555

AN:

222208

Hom.:

AF XY:

0.00532

AC XY:

634

AN XY:

119126

show subpopulations

Gnomad AFR exome

AF:

0.0853

Gnomad AMR exome

AF:

0.00709

Gnomad ASJ exome

AF:

0.00106

Gnomad EAS exome

AF:

0.000238

Gnomad SAS exome

AF:

0.0000745

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00111

Gnomad OTH exome

AF:

0.00357

GnomAD4 exome

AF:

0.00328

AC:

4741

AN:

1443634

Hom.:

137

Cov.:

AF XY:

0.00302

AC XY:

2163

AN XY:

716094

show subpopulations

Gnomad4 AFR exome

AF:

0.0867

Gnomad4 AMR exome

AF:

0.00731

Gnomad4 ASJ exome

AF:

0.00140

Gnomad4 EAS exome

AF:

0.000307

Gnomad4 SAS exome

AF:

0.000253

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000953

Gnomad4 OTH exome

AF:

0.00653

GnomAD4 genome

AF:

0.0244

AC:

3715

AN:

152200

Hom.:

161

Cov.:

AF XY:

0.0241

AC XY:

1790

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0827

Gnomad4 AMR

AF:

0.0103

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000985

Gnomad4 OTH

AF:

0.0199

Alfa

AF:

0.00520

Hom.:

Bravo

AF:

0.0282

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.00104

AC:

ESP6500AA

AF:

0.0867

AC:

382

ESP6500EA

AF:

0.000930

AC:

ExAC

AF:

0.00751

AC:

910

Asia WGS

AF:

0.00520

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 29, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 22, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 03, 2018	This variant is associated with the following publications: (PMID: 25525159, 27013732, 20981092, 15509590, 16123375) -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jul 23, 2013	- -

Maturity onset diabetes mellitus in young

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Monogenic diabetes

Benign:1

Benign, criteria provided, single submitter

research

Personalized Diabetes Medicine Program, University of Maryland School of Medicine

Sep 22, 2017

ACMG Criteria:BS1 (9% MAF in Africans in 1000g), BS2 (194 controls and 198 cases in type2diabetesgenetics.org) + BP4, PP3 +BP6 (called benign by Chicago). Notes: May be causal in homozygous state. Susceptibility when homozygous (PMID 15509590), 37 hets and 3 homozygotes in 495 TODAY study -

Diabetes mellitus, ketosis-prone, susceptibility to

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Dec 15, 2004

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.36

BayesDel_noAF

Benign

-0.23

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.065

.;.;.;.;.;T

Eigen

Benign

-0.034

Eigen_PC

Benign

-0.0048

FATHMM_MKL

Uncertain

0.79

LIST_S2

Benign

0.62

T;T;T;T;.;T

MetaRNN

Benign

0.0025

T;T;T;T;T;T

MetaSVM

Benign

-0.60

MutationTaster

Benign

1.0

N;N;N;N

PrimateAI

Benign

0.31

PROVEAN

Benign

1.2

N;.;N;N;N;.

REVEL

Uncertain

0.32

Sift

Benign

0.035

D;.;D;D;D;.

Sift4G

Uncertain

0.021

D;.;.;D;D;D

Polyphen

0.83

P;.;.;.;P;.

Vest4

0.20

MVP

0.96

MPC

0.15

ClinPred

0.036

GERP RS

5.1

gMVP

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.13

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