7-127610868-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000378740.6(PAX4):c.1031C>T(p.Thr344Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000793 in 1,386,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000378740.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAX4 | NM_001366110.1 | c.*196C>T | 3_prime_UTR_variant | 12/12 | ENST00000639438.3 | NP_001353039.1 | ||
PAX4 | NM_001366111.1 | c.1031C>T | p.Thr344Ile | missense_variant | 10/10 | NP_001353040.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAX4 | ENST00000378740.6 | c.1031C>T | p.Thr344Ile | missense_variant | 10/10 | 1 | ENSP00000368014 | P2 | ||
PAX4 | ENST00000639438.3 | c.*196C>T | 3_prime_UTR_variant | 12/12 | 5 | NM_001366110.1 | ENSP00000491782 | A2 | ||
PAX4 | ENST00000341640.6 | c.*196C>T | 3_prime_UTR_variant | 9/9 | 1 | ENSP00000339906 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000215 AC: 3AN: 139812Hom.: 0 AF XY: 0.0000132 AC XY: 1AN XY: 75756
GnomAD4 exome AF: 0.00000793 AC: 11AN: 1386614Hom.: 0 Cov.: 56 AF XY: 0.00000877 AC XY: 6AN XY: 684258
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 12, 2023 | Variant summary: PAX4 c.*196C>T is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 2.1e-05 in 139812 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.*196C>T in individuals affected with Monogenic Diabetes and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at