7-127610874-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000378740.6(PAX4):c.1025C>T(p.Thr342Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000723 in 1,539,682 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000378740.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAX4 | NM_001366110.1 | c.*190C>T | 3_prime_UTR_variant | 12/12 | ENST00000639438.3 | NP_001353039.1 | ||
PAX4 | NM_001366111.1 | c.1025C>T | p.Thr342Ile | missense_variant | 10/10 | NP_001353040.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAX4 | ENST00000378740.6 | c.1025C>T | p.Thr342Ile | missense_variant | 10/10 | 1 | ENSP00000368014 | P2 | ||
PAX4 | ENST00000639438.3 | c.*190C>T | 3_prime_UTR_variant | 12/12 | 5 | NM_001366110.1 | ENSP00000491782 | A2 | ||
PAX4 | ENST00000341640.6 | c.*190C>T | 3_prime_UTR_variant | 9/9 | 1 | ENSP00000339906 |
Frequencies
GnomAD3 genomes AF: 0.00394 AC: 599AN: 152216Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00100 AC: 141AN: 140410Hom.: 1 AF XY: 0.000697 AC XY: 53AN XY: 76038
GnomAD4 exome AF: 0.000370 AC: 514AN: 1387348Hom.: 7 Cov.: 55 AF XY: 0.000307 AC XY: 210AN XY: 684600
GnomAD4 genome AF: 0.00393 AC: 599AN: 152334Hom.: 4 Cov.: 33 AF XY: 0.00375 AC XY: 279AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 31, 2022 | - - |
PAX4-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 26, 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
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at