rs17257120
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152835.5(PDIK1L):c.*1033A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,602 control chromosomes in the GnomAD database, including 2,268 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.17 ( 2267 hom., cov: 32)
Exomes 𝑓: 0.13 ( 1 hom. )
Consequence
PDIK1L
NM_152835.5 3_prime_UTR
NM_152835.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.21
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDIK1L | NM_152835.5 | c.*1033A>G | 3_prime_UTR_variant | 3/3 | ENST00000374269.2 | ||
PDIK1L | NM_001243532.2 | c.*1033A>G | 3_prime_UTR_variant | 3/3 | |||
PDIK1L | NM_001243533.2 | c.*1033A>G | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDIK1L | ENST00000374269.2 | c.*1033A>G | 3_prime_UTR_variant | 3/3 | 1 | NM_152835.5 | P1 | ||
PDIK1L | ENST00000374271.8 | c.*1033A>G | 3_prime_UTR_variant | 4/4 | 1 | P1 | |||
PDIK1L | ENST00000619836.4 | c.*1033A>G | 3_prime_UTR_variant | 3/3 | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.166 AC: 25181AN: 152044Hom.: 2268 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.134 AC: 59AN: 440Hom.: 1 Cov.: 0 AF XY: 0.152 AC XY: 40AN XY: 264
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GnomAD4 genome ? AF: 0.166 AC: 25185AN: 152162Hom.: 2267 Cov.: 32 AF XY: 0.160 AC XY: 11893AN XY: 74386
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at