7-127614497-G-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001366110.1(PAX4):c.421C>A(p.Arg141=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000208 in 1,443,648 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
PAX4
NM_001366110.1 synonymous
NM_001366110.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.67
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX4 | NM_001366110.1 | c.421C>A | p.Arg141= | synonymous_variant | 6/12 | ENST00000639438.3 | |
PAX4 | NM_001366111.1 | c.421C>A | p.Arg141= | synonymous_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX4 | ENST00000639438.3 | c.421C>A | p.Arg141= | synonymous_variant | 6/12 | 5 | NM_001366110.1 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000450 AC: 1AN: 222208Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 119126
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GnomAD4 exome AF: 0.00000208 AC: 3AN: 1443648Hom.: 0 Cov.: 32 AF XY: 0.00000140 AC XY: 1AN XY: 716100
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GnomAD4 genome Cov.: 32
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32
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at