7-127610546-AGT-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001366110.1(PAX4):​c.*516_*517del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 200,804 control chromosomes in the GnomAD database, including 17 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0078 ( 15 hom., cov: 0)
Exomes 𝑓: 0.063 ( 2 hom. )

Consequence

PAX4
NM_001366110.1 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.286
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PAX4NM_001366110.1 linkuse as main transcriptc.*516_*517del 3_prime_UTR_variant 12/12 ENST00000639438.3 NP_001353039.1
PAX4NM_001366111.1 linkuse as main transcriptc.*304_*305del 3_prime_UTR_variant 10/10 NP_001353040.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PAX4ENST00000639438.3 linkuse as main transcriptc.*516_*517del 3_prime_UTR_variant 12/125 NM_001366110.1 ENSP00000491782 A2
PAX4ENST00000341640.6 linkuse as main transcriptc.*516_*517del 3_prime_UTR_variant 9/91 ENSP00000339906 O43316-4

Frequencies

GnomAD3 genomes
AF:
0.00776
AC:
1102
AN:
142062
Hom.:
15
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0257
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00321
Gnomad ASJ
AF:
0.000588
Gnomad EAS
AF:
0.000201
Gnomad SAS
AF:
0.00456
Gnomad FIN
AF:
0.000614
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00125
Gnomad OTH
AF:
0.00673
GnomAD4 exome
AF:
0.0630
AC:
3692
AN:
58642
Hom.:
2
AF XY:
0.0632
AC XY:
1933
AN XY:
30568
show subpopulations
Gnomad4 AFR exome
AF:
0.0616
Gnomad4 AMR exome
AF:
0.0520
Gnomad4 ASJ exome
AF:
0.0518
Gnomad4 EAS exome
AF:
0.107
Gnomad4 SAS exome
AF:
0.0655
Gnomad4 FIN exome
AF:
0.0651
Gnomad4 NFE exome
AF:
0.0567
Gnomad4 OTH exome
AF:
0.0657
GnomAD4 genome
AF:
0.00780
AC:
1109
AN:
142162
Hom.:
15
Cov.:
0
AF XY:
0.00772
AC XY:
535
AN XY:
69302
show subpopulations
Gnomad4 AFR
AF:
0.0259
Gnomad4 AMR
AF:
0.00320
Gnomad4 ASJ
AF:
0.000588
Gnomad4 EAS
AF:
0.000202
Gnomad4 SAS
AF:
0.00410
Gnomad4 FIN
AF:
0.000614
Gnomad4 NFE
AF:
0.00125
Gnomad4 OTH
AF:
0.00667

ClinVar

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

Submissions by phenotype

Maturity onset diabetes mellitus in young Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs36159526; hg19: chr7-127250600; API