7-127610586-C-CACAT

Variant summary

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

The NM_001366110.1(PAX4):​c.*477_*478insATGT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 401,558 control chromosomes in the GnomAD database, including 28,303 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.40 ( 8243 hom., cov: 32)
Exomes 𝑓: 0.35 ( 20060 hom. )

Consequence

PAX4
NM_001366110.1 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.601
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 7-127610586-C-CACAT is Benign according to our data. Variant chr7-127610586-C-CACAT is described in ClinVar as [Benign]. Clinvar id is 358785.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PAX4NM_001366110.1 linkuse as main transcriptc.*477_*478insATGT 3_prime_UTR_variant 12/12 ENST00000639438.3 NP_001353039.1
PAX4NM_001366111.1 linkuse as main transcriptc.*265_*266insATGT 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.*477_*478insATGT 3_prime_UTR_variant 12/125 NM_001366110.1 ENSP00000491782 A2
PAX4ENST00000341640.6 linkuse as main transcriptc.*477_*478insATGT 3_prime_UTR_variant 9/91 ENSP00000339906 O43316-4

Frequencies

GnomAD3 genomes
AF:
0.396
AC:
45478
AN:
114758
Hom.:
8234
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.191
Gnomad AMI
AF:
0.496
Gnomad AMR
AF:
0.472
Gnomad ASJ
AF:
0.582
Gnomad EAS
AF:
0.115
Gnomad SAS
AF:
0.396
Gnomad FIN
AF:
0.381
Gnomad MID
AF:
0.562
Gnomad NFE
AF:
0.478
Gnomad OTH
AF:
0.420
GnomAD4 exome
AF:
0.351
AC:
100666
AN:
286736
Hom.:
20060
Cov.:
0
AF XY:
0.348
AC XY:
52775
AN XY:
151438
show subpopulations
Gnomad4 AFR exome
AF:
0.109
Gnomad4 AMR exome
AF:
0.425
Gnomad4 ASJ exome
AF:
0.496
Gnomad4 EAS exome
AF:
0.0985
Gnomad4 SAS exome
AF:
0.301
Gnomad4 FIN exome
AF:
0.287
Gnomad4 NFE exome
AF:
0.396
Gnomad4 OTH exome
AF:
0.363
GnomAD4 genome
AF:
0.396
AC:
45499
AN:
114822
Hom.:
8243
Cov.:
32
AF XY:
0.390
AC XY:
21927
AN XY:
56162
show subpopulations
Gnomad4 AFR
AF:
0.190
Gnomad4 AMR
AF:
0.472
Gnomad4 ASJ
AF:
0.582
Gnomad4 EAS
AF:
0.115
Gnomad4 SAS
AF:
0.397
Gnomad4 FIN
AF:
0.381
Gnomad4 NFE
AF:
0.478
Gnomad4 OTH
AF:
0.423
Alfa
AF:
0.0834
Hom.:
213
Asia WGS
AF:
0.221
AC:
762
AN:
3460

ClinVar

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

Submissions by phenotype

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

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs200757052; hg19: chr7-127250640; API