7-127610570-T-TGTGC

Variant summary

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

The NM_001366110.1(PAX4):​c.*493_*494insGCAC 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 0.020 ( 67 hom., cov: 18)
Exomes 𝑓: 0.0027 ( 1 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-TGTGC is Benign according to our data. Variant chr7-127610570-T-TGTGC is described in ClinVar as [Likely_benign]. Clinvar id is 358783.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0528 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_*494insGCAC 3_prime_UTR_variant 12/12 ENST00000639438.3 NP_001353039.1
PAX4NM_001366111.1 linkuse as main transcriptc.*281_*282insGCAC 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_*494insGCAC 3_prime_UTR_variant 12/125 NM_001366110.1 ENSP00000491782 A2
PAX4ENST00000341640.6 linkuse as main transcriptc.*493_*494insGCAC 3_prime_UTR_variant 9/91 ENSP00000339906 O43316-4

Frequencies

GnomAD3 genomes
AF:
0.0198
AC:
2600
AN:
131620
Hom.:
67
Cov.:
18
show subpopulations
Gnomad AFR
AF:
0.0548
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00859
Gnomad ASJ
AF:
0.0132
Gnomad EAS
AF:
0.0113
Gnomad SAS
AF:
0.0106
Gnomad FIN
AF:
0.00938
Gnomad MID
AF:
0.00431
Gnomad NFE
AF:
0.00188
Gnomad OTH
AF:
0.0154
GnomAD4 exome
AF:
0.00270
AC:
511
AN:
188962
Hom.:
1
Cov.:
0
AF XY:
0.00282
AC XY:
282
AN XY:
99978
show subpopulations
Gnomad4 AFR exome
AF:
0.0216
Gnomad4 AMR exome
AF:
0.00235
Gnomad4 ASJ exome
AF:
0.00517
Gnomad4 EAS exome
AF:
0.00584
Gnomad4 SAS exome
AF:
0.00399
Gnomad4 FIN exome
AF:
0.00246
Gnomad4 NFE exome
AF:
0.00102
Gnomad4 OTH exome
AF:
0.00242
GnomAD4 genome
AF:
0.0197
AC:
2598
AN:
131718
Hom.:
67
Cov.:
18
AF XY:
0.0196
AC XY:
1262
AN XY:
64296
show subpopulations
Gnomad4 AFR
AF:
0.0547
Gnomad4 AMR
AF:
0.00858
Gnomad4 ASJ
AF:
0.0132
Gnomad4 EAS
AF:
0.0112
Gnomad4 SAS
AF:
0.00995
Gnomad4 FIN
AF:
0.00938
Gnomad4 NFE
AF:
0.00188
Gnomad4 OTH
AF:
0.0147
Alfa
AF:
0.000930
Hom.:
0

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: rs375106423; hg19: chr7-127250624; API