rs535090775
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_178161.3(PTF1A):āc.269G>Cā(p.Gly90Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000855 in 1,315,372 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_178161.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTF1A | NM_178161.3 | c.269G>C | p.Gly90Ala | missense_variant | 1/2 | ENST00000376504.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTF1A | ENST00000376504.4 | c.269G>C | p.Gly90Ala | missense_variant | 1/2 | 1 | NM_178161.3 | P1 | |
PTF1A | ENST00000638469.1 | c.114+122G>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00397 AC: 603AN: 151806Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000834 AC: 10AN: 11992Hom.: 0 AF XY: 0.000540 AC XY: 4AN XY: 7410
GnomAD4 exome AF: 0.000448 AC: 521AN: 1163458Hom.: 0 Cov.: 32 AF XY: 0.000418 AC XY: 234AN XY: 560076
GnomAD4 genome ? AF: 0.00397 AC: 603AN: 151914Hom.: 0 Cov.: 32 AF XY: 0.00389 AC XY: 289AN XY: 74260
ClinVar
Submissions by phenotype
Permanent neonatal diabetes mellitus-pancreatic and cerebellar agenesis syndrome;C4014737:Pancreatic agenesis 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Pancreatic agenesis 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Feb 09, 2021 | - - |
Monogenic diabetes Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Personalized Diabetes Medicine Program, University of Maryland School of Medicine | Oct 27, 2015 | ACMG Criteria: BP4 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 07, 2019 | - - |
Permanent neonatal diabetes mellitus-pancreatic and cerebellar agenesis syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at