7-127610662-A-G

Variant summary

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

The NM_001366110.1(PAX4):​c.*402T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0286 in 596,872 control chromosomes in the GnomAD database, including 1,570 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.072 ( 1172 hom., cov: 34)
Exomes 𝑓: 0.014 ( 398 hom. )

Consequence

PAX4
NM_001366110.1 3_prime_UTR

Scores

2

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.25
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 7-127610662-A-G is Benign according to our data. Variant chr7-127610662-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 358789.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PAX4NM_001366110.1 linkuse as main transcriptc.*402T>C 3_prime_UTR_variant 12/12 ENST00000639438.3 NP_001353039.1
PAX4NM_001366111.1 linkuse as main transcriptc.*190T>C 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.*402T>C 3_prime_UTR_variant 12/125 NM_001366110.1 ENSP00000491782 A2
PAX4ENST00000341640.6 linkuse as main transcriptc.*402T>C 3_prime_UTR_variant 9/91 ENSP00000339906 O43316-4

Frequencies

GnomAD3 genomes
AF:
0.0717
AC:
10913
AN:
152198
Hom.:
1164
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.232
Gnomad AMI
AF:
0.0252
Gnomad AMR
AF:
0.0534
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0413
Gnomad SAS
AF:
0.00538
Gnomad FIN
AF:
0.000376
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00160
Gnomad OTH
AF:
0.0554
GnomAD4 exome
AF:
0.0137
AC:
6101
AN:
444556
Hom.:
398
Cov.:
3
AF XY:
0.0119
AC XY:
2783
AN XY:
233994
show subpopulations
Gnomad4 AFR exome
AF:
0.226
Gnomad4 AMR exome
AF:
0.0459
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0399
Gnomad4 SAS exome
AF:
0.00386
Gnomad4 FIN exome
AF:
0.00111
Gnomad4 NFE exome
AF:
0.00132
Gnomad4 OTH exome
AF:
0.0246
GnomAD4 genome
AF:
0.0718
AC:
10942
AN:
152316
Hom.:
1172
Cov.:
34
AF XY:
0.0693
AC XY:
5162
AN XY:
74510
show subpopulations
Gnomad4 AFR
AF:
0.232
Gnomad4 AMR
AF:
0.0532
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0412
Gnomad4 SAS
AF:
0.00538
Gnomad4 FIN
AF:
0.000376
Gnomad4 NFE
AF:
0.00160
Gnomad4 OTH
AF:
0.0549
Alfa
AF:
0.0427
Hom.:
138
Bravo
AF:
0.0837
Asia WGS
AF:
0.0330
AC:
116
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
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- -
not provided Benign:1
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
7.8
DANN
Benign
0.46

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: rs327519; hg19: chr7-127250716; API