7-127610853-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBA1
The ENST00000378740.6(PAX4):āc.1046A>Gā(p.Ter349TrpextTer2) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 1,536,282 control chromosomes in the GnomAD database, including 456,085 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.74 ( 42467 hom., cov: 32)
Exomes š: 0.77 ( 413618 hom. )
Consequence
PAX4
ENST00000378740.6 stop_lost
ENST00000378740.6 stop_lost
Scores
7
Clinical Significance
Conservation
PhyloP100: -0.00600
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 -14 ACMG points.
PM4
Stoplost variant in ENST00000378740.6 Downstream stopcodon found after 8 codons.
BP6
Variant 7-127610853-T-C is Benign according to our data. Variant chr7-127610853-T-C is described in ClinVar as [Benign]. Clinvar id is 358791.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-127610853-T-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAX4 | NM_001366110.1 | c.*211A>G | 3_prime_UTR_variant | 12/12 | ENST00000639438.3 | NP_001353039.1 | ||
PAX4 | NM_001366111.1 | c.1046A>G | p.Ter349TrpextTer2 | stop_lost | 10/10 | NP_001353040.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAX4 | ENST00000378740.6 | c.1046A>G | p.Ter349TrpextTer2 | stop_lost | 10/10 | 1 | ENSP00000368014 | P2 | ||
PAX4 | ENST00000639438.3 | c.*211A>G | 3_prime_UTR_variant | 12/12 | 5 | NM_001366110.1 | ENSP00000491782 | A2 | ||
PAX4 | ENST00000341640.6 | c.*211A>G | 3_prime_UTR_variant | 9/9 | 1 | ENSP00000339906 |
Frequencies
GnomAD3 genomes AF: 0.743 AC: 112892AN: 152022Hom.: 42440 Cov.: 32
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GnomAD3 exomes AF: 0.734 AC: 101797AN: 138708Hom.: 38217 AF XY: 0.736 AC XY: 55398AN XY: 75220
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GnomAD4 exome AF: 0.769 AC: 1064249AN: 1384142Hom.: 413618 Cov.: 36 AF XY: 0.768 AC XY: 524459AN XY: 683108
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GnomAD4 genome AF: 0.743 AC: 112969AN: 152140Hom.: 42467 Cov.: 32 AF XY: 0.736 AC XY: 54772AN XY: 74382
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 09, 2018 | - - |
Type 2 diabetes mellitus Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
PAX4-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 25, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Maturity onset diabetes mellitus in young Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
P;P;P
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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