7-127610546-A-AGT
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001366110.1(PAX4):c.*517_*518insAC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.36 ( 9425 hom., cov: 0)
Exomes 𝑓: 0.24 ( 298 hom. )
Consequence
PAX4
NM_001366110.1 3_prime_UTR
NM_001366110.1 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.286
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 -8 ACMG points.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAX4 | NM_001366110.1 | c.*517_*518insAC | 3_prime_UTR_variant | 12/12 | ENST00000639438.3 | NP_001353039.1 | ||
PAX4 | NM_001366111.1 | c.*305_*306insAC | 3_prime_UTR_variant | 10/10 | NP_001353040.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAX4 | ENST00000639438.3 | c.*517_*518insAC | 3_prime_UTR_variant | 12/12 | 5 | NM_001366110.1 | ENSP00000491782 | A2 | ||
PAX4 | ENST00000341640.6 | c.*517_*518insAC | 3_prime_UTR_variant | 9/9 | 1 | ENSP00000339906 |
Frequencies
GnomAD3 genomes AF: 0.359 AC: 50966AN: 142014Hom.: 9417 Cov.: 0
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GnomAD4 exome AF: 0.242 AC: 14753AN: 61078Hom.: 298 Cov.: 0 AF XY: 0.242 AC XY: 7722AN XY: 31846
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GnomAD4 genome AF: 0.359 AC: 50996AN: 142114Hom.: 9425 Cov.: 0 AF XY: 0.354 AC XY: 24504AN XY: 69268
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Maturity onset diabetes mellitus in young Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at