ENST00000493544.1:n.4678G>A

Variant names:

• chr2-241114131-C-T
• rs17382723
• ENST00000493544.1:n.4678G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000493544.1(PASK):​n.4678G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: PASK ENST00000493544.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000493544.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PASK	NM_015148.4	MANE Select	c.3333+912G>A		intron	N/A	NP_055963.2
	PASK	NM_001252124.2		c.*813G>A		3_prime_UTR	Exon 14 of 14	NP_001239053.1
	PASK	NM_001252119.2		c.3354+891G>A		intron	N/A	NP_001239048.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PASK	ENST00000493544.1	TSL:1	n.4678G>A		non_coding_transcript_exon	Exon 6 of 6
	PASK	ENST00000403638.7	TSL:1	c.*813G>A		3_prime_UTR	Exon 14 of 14	ENSP00000384438.3
	PASK	ENST00000234040.9	TSL:1 MANE Select	c.3333+912G>A		intron	N/A	ENSP00000234040.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 419

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.77
DANN	Benign	0.75
PhyloP100		-0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17382723; hg19: chr2-242053546;