10-87863174-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001126049.2(KLLN):c.-687C>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 186,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001126049.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLLN | NM_001126049.2 | c.-687C>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 1 | ENST00000445946.5 | NP_001119521.1 | ||
KLLN | NM_001126049.2 | c.-687C>A | 5_prime_UTR_variant | Exon 1 of 1 | ENST00000445946.5 | NP_001119521.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLLN | ENST00000445946.5 | c.-687C>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 1 | 6 | NM_001126049.2 | ENSP00000392204.2 | |||
KLLN | ENST00000445946.5 | c.-687C>A | 5_prime_UTR_variant | Exon 1 of 1 | 6 | NM_001126049.2 | ENSP00000392204.2 | |||
PTEN | ENST00000688308.1 | c.-17+61G>T | intron_variant | Intron 1 of 9 | ENSP00000508752.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000588 AC: 2AN: 34006Hom.: 0 Cov.: 0 AF XY: 0.0000617 AC XY: 1AN XY: 16212
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74312
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant is denoted PTEN c.-1296G>T, and describes a nucleotide substitution 1296 base pairs upstream of the ATG translational start site in the PTEN promoter region. The surrounding sequence, with the base that is substituted in brackets, is ATCA[G/T]TCCT. This variant, also defined as c.-1295G>T using alternate numbering, has not, to our knowledge, been published in the literature as pathogenic or benign. PTEN c.-1296G>T was not observed at a significant allele frequency in large population cohorts (Lek 2016). Variants within the PTEN promoter have been observed in individuals with features of Cowden syndrome (Zhou 2003). At this time, we consider this to be a variant of uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at