10-87966988-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000314.8(PTEN):c.*1516T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 218,680 control chromosomes in the GnomAD database, including 15,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000314.8 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTEN | NM_000314.8 | c.*1516T>C | 3_prime_UTR_variant | Exon 9 of 9 | ENST00000371953.8 | NP_000305.3 | ||
PTEN | NM_001304717.5 | c.*1516T>C | 3_prime_UTR_variant | Exon 10 of 10 | NP_001291646.4 | |||
PTEN | NM_001304718.2 | c.*1516T>C | 3_prime_UTR_variant | Exon 9 of 9 | NP_001291647.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.341 AC: 49462AN: 145100Hom.: 9530 Cov.: 24
GnomAD4 exome AF: 0.394 AC: 28976AN: 73494Hom.: 5779 Cov.: 0 AF XY: 0.398 AC XY: 13549AN XY: 34062
GnomAD4 genome AF: 0.341 AC: 49456AN: 145186Hom.: 9528 Cov.: 24 AF XY: 0.349 AC XY: 24459AN XY: 70168
ClinVar
Submissions by phenotype
PTEN hamartoma tumor syndrome Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at