7-127610570-T-TGC

Variant summary

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

The NM_001366110.1(PAX4):​c.*493_*494insGC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.23 ( 3019 hom., cov: 18)
Exomes 𝑓: 0.14 ( 2427 hom. )

Consequence

PAX4
NM_001366110.1 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.415
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 7-127610570-T-TGC is Benign according to our data. Variant chr7-127610570-T-TGC is described in ClinVar as [Likely_benign]. Clinvar id is 358782.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PAX4NM_001366110.1 linkuse as main transcriptc.*493_*494insGC 3_prime_UTR_variant 12/12 ENST00000639438.3 NP_001353039.1
PAX4NM_001366111.1 linkuse as main transcriptc.*281_*282insGC 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.*493_*494insGC 3_prime_UTR_variant 12/125 NM_001366110.1 ENSP00000491782 A2
PAX4ENST00000341640.6 linkuse as main transcriptc.*493_*494insGC 3_prime_UTR_variant 9/91 ENSP00000339906 O43316-4

Frequencies

GnomAD3 genomes
AF:
0.229
AC:
30112
AN:
131484
Hom.:
3017
Cov.:
18
show subpopulations
Gnomad AFR
AF:
0.209
Gnomad AMI
AF:
0.158
Gnomad AMR
AF:
0.217
Gnomad ASJ
AF:
0.216
Gnomad EAS
AF:
0.137
Gnomad SAS
AF:
0.326
Gnomad FIN
AF:
0.208
Gnomad MID
AF:
0.172
Gnomad NFE
AF:
0.251
Gnomad OTH
AF:
0.228
GnomAD4 exome
AF:
0.145
AC:
26332
AN:
181612
Hom.:
2427
Cov.:
0
AF XY:
0.149
AC XY:
14324
AN XY:
96050
show subpopulations
Gnomad4 AFR exome
AF:
0.163
Gnomad4 AMR exome
AF:
0.103
Gnomad4 ASJ exome
AF:
0.106
Gnomad4 EAS exome
AF:
0.0759
Gnomad4 SAS exome
AF:
0.204
Gnomad4 FIN exome
AF:
0.130
Gnomad4 NFE exome
AF:
0.146
Gnomad4 OTH exome
AF:
0.135
GnomAD4 genome
AF:
0.229
AC:
30127
AN:
131580
Hom.:
3019
Cov.:
18
AF XY:
0.228
AC XY:
14653
AN XY:
64218
show subpopulations
Gnomad4 AFR
AF:
0.209
Gnomad4 AMR
AF:
0.217
Gnomad4 ASJ
AF:
0.216
Gnomad4 EAS
AF:
0.136
Gnomad4 SAS
AF:
0.325
Gnomad4 FIN
AF:
0.208
Gnomad4 NFE
AF:
0.251
Gnomad4 OTH
AF:
0.227

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

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: rs61297182; hg19: chr7-127250624; API