rs769235876
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 16P and 4B. PVS1PP5_Very_StrongBS2
The NM_016953.4(PDE11A):c.2268_2272del(p.Ser757GlnfsTer4) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000264 in 1,591,772 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. L756L) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_016953.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE11A | NM_016953.4 | c.2268_2272del | p.Ser757GlnfsTer4 | frameshift_variant | 15/20 | ENST00000286063.11 | |
PDE11A-AS1 | NR_136171.1 | n.105-1021_105-1017del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE11A | ENST00000286063.11 | c.2268_2272del | p.Ser757GlnfsTer4 | frameshift_variant | 15/20 | 1 | NM_016953.4 | P1 | |
PDE11A-AS1 | ENST00000653062.1 | n.366-1021_366-1017del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152104Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000956 AC: 24AN: 251006Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135636
GnomAD4 exome AF: 0.0000250 AC: 36AN: 1439550Hom.: 0 AF XY: 0.0000251 AC XY: 18AN XY: 717664
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74422
ClinVar
Submissions by phenotype
Pigmented nodular adrenocortical disease, primary, 2 Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Likely pathogenic, criteria provided, single submitter | reference population | Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center | Mar 18, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at