2-177817928-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_016953.4(PDE11A):c.1577-3T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 1,396,904 control chromosomes in the GnomAD database, including 75,446 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_016953.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDE11A | NM_016953.4 | c.1577-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000286063.11 | |||
PDE11A | NM_001077196.2 | c.245-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
PDE11A | NM_001077197.2 | c.827-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
PDE11A | NM_001077358.2 | c.503-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDE11A | ENST00000286063.11 | c.1577-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_016953.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.406 AC: 61646AN: 151786Hom.: 14355 Cov.: 31
GnomAD3 exomes AF: 0.324 AC: 81066AN: 250122Hom.: 14669 AF XY: 0.325 AC XY: 43891AN XY: 135210
GnomAD4 exome AF: 0.305 AC: 380217AN: 1245000Hom.: 61075 Cov.: 20 AF XY: 0.308 AC XY: 194133AN XY: 630134
GnomAD4 genome AF: 0.406 AC: 61704AN: 151904Hom.: 14371 Cov.: 31 AF XY: 0.400 AC XY: 29705AN XY: 74254
ClinVar
Submissions by phenotype
Pigmented nodular adrenocortical disease, primary, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at