rs17382723
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000403638.7(PASK):c.*813G>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 0.207 in 984,670 control chromosomes in the GnomAD database, including 21,689 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 0.18 ( 2735 hom., cov: 33)
Exomes 𝑓: 0.21 ( 18954 hom. )
Consequence
PASK
ENST00000403638.7 3_prime_UTR
ENST00000403638.7 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.298
Genes affected
PASK (HGNC:17270): (PAS domain containing serine/threonine kinase) This gene encodes a member of the serine/threonine kinase family that contains two PAS domains. Expression of this gene is regulated by glucose, and the encoded protein plays a role in the regulation of insulin gene expression. Downregulation of this gene may play a role in type 2 diabetes. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PASK | NM_015148.4 | c.3333+912G>C | intron_variant | ENST00000234040.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PASK | ENST00000234040.9 | c.3333+912G>C | intron_variant | 1 | NM_015148.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.181 AC: 27534AN: 152038Hom.: 2739 Cov.: 33
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GnomAD4 exome AF: 0.212 AC: 176509AN: 832514Hom.: 18954 Cov.: 28 AF XY: 0.212 AC XY: 81380AN XY: 384450
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GnomAD4 genome ? AF: 0.181 AC: 27538AN: 152156Hom.: 2735 Cov.: 33 AF XY: 0.178 AC XY: 13272AN XY: 74366
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ClinVar
Not reported inComputational scores
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Name
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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