7-127610393-CAT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001366110.1(PAX4):​c.*669_*670del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0548 in 158,650 control chromosomes in the GnomAD database, including 704 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.057 ( 701 hom., cov: 32)
Exomes 𝑓: 0.010 ( 3 hom. )

Consequence

PAX4
NM_001366110.1 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0850
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 -10 ACMG points.

BP6
Variant 7-127610393-CAT-C is Benign according to our data. Variant chr7-127610393-CAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 358774.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PAX4NM_001366110.1 linkuse as main transcriptc.*669_*670del 3_prime_UTR_variant 12/12 ENST00000639438.3 NP_001353039.1
PAX4NM_001366111.1 linkuse as main transcriptc.*457_*458del 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.*669_*670del 3_prime_UTR_variant 12/125 NM_001366110.1 ENSP00000491782 A2
PAX4ENST00000341640.6 linkuse as main transcriptc.*669_*670del 3_prime_UTR_variant 9/91 ENSP00000339906 O43316-4

Frequencies

GnomAD3 genomes
AF:
0.0567
AC:
8610
AN:
151912
Hom.:
696
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.179
Gnomad AMI
AF:
0.0252
Gnomad AMR
AF:
0.0467
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0415
Gnomad SAS
AF:
0.00539
Gnomad FIN
AF:
0.000378
Gnomad MID
AF:
0.0159
Gnomad NFE
AF:
0.00152
Gnomad OTH
AF:
0.0480
GnomAD4 exome
AF:
0.0103
AC:
68
AN:
6622
Hom.:
3
AF XY:
0.0111
AC XY:
38
AN XY:
3432
show subpopulations
Gnomad4 AFR exome
AF:
0.196
Gnomad4 AMR exome
AF:
0.0252
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0455
Gnomad4 SAS exome
AF:
0.00485
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00102
Gnomad4 OTH exome
AF:
0.00481
GnomAD4 genome
AF:
0.0568
AC:
8632
AN:
152028
Hom.:
701
Cov.:
32
AF XY:
0.0554
AC XY:
4120
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.179
Gnomad4 AMR
AF:
0.0466
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0414
Gnomad4 SAS
AF:
0.00540
Gnomad4 FIN
AF:
0.000378
Gnomad4 NFE
AF:
0.00152
Gnomad4 OTH
AF:
0.0475
Alfa
AF:
0.0326
Hom.:
54
Bravo
AF:
0.0669
Asia WGS
AF:
0.0320
AC:
111
AN:
3478

ClinVar

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

Submissions by phenotype

Maturity onset diabetes mellitus in young Benign:1
Likely benign, 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: rs59241875; hg19: chr7-127250447; API