7-127610543-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001366110.1(PAX4):c.*521C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 228,788 control chromosomes in the GnomAD database, including 62,305 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.74 ( 42461 hom., cov: 33)
Exomes 𝑓: 0.69 ( 19844 hom. )
Consequence
PAX4
NM_001366110.1 3_prime_UTR
NM_001366110.1 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00200
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 7-127610543-G-A is Benign according to our data. Variant chr7-127610543-G-A is described in ClinVar as [Benign]. Clinvar id is 358778.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX4 | NM_001366110.1 | c.*521C>T | 3_prime_UTR_variant | 12/12 | ENST00000639438.3 | ||
PAX4 | NM_001366111.1 | c.*309C>T | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX4 | ENST00000639438.3 | c.*521C>T | 3_prime_UTR_variant | 12/12 | 5 | NM_001366110.1 | A2 | ||
PAX4 | ENST00000341640.6 | c.*521C>T | 3_prime_UTR_variant | 9/9 | 1 |
Frequencies
GnomAD3 genomes AF: 0.744 AC: 112871AN: 151774Hom.: 42435 Cov.: 33
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GnomAD4 exome AF: 0.690 AC: 53072AN: 76894Hom.: 19844 Cov.: 0 AF XY: 0.690 AC XY: 27730AN XY: 40170
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GnomAD4 genome AF: 0.744 AC: 112947AN: 151894Hom.: 42461 Cov.: 33 AF XY: 0.738 AC XY: 54758AN XY: 74244
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ClinVar
Significance: 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
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at