20-44581194-T-C

Position:

• chr20-44581194-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000372894.7(PKIG):​c.-93-8603T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,088 control chromosomes in the GnomAD database, including 15,677 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 0.42 (15677 hom., cov: 32)
• Consequence: PKIG ENST00000372894.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

Genes affected

PKIG (HGNC:9019): (cAMP-dependent protein kinase inhibitor gamma) This gene encodes a member of the protein kinase inhibitor family. Studies of a similar protein in mice suggest that this protein acts as a potent competitive cAMP-dependent protein kinase inhibitor, and is a predominant form of inhibitor in various tissues. The encoded protein may be involved in osteogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKIG	NM_001281444.2	c.-515-1391T>C		intron_variant			NP_001268373.1
PKIG	NM_007066.5	c.-93-8603T>C		intron_variant			NP_008997.1
PKIG	NM_181804.3	c.-240-1391T>C		intron_variant			NP_861520.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKIG	ENST00000372894.7	c.-93-8603T>C		intron_variant		1		ENSP00000361985	P1
PKIG	ENST00000372887.5	c.-240-1391T>C		intron_variant		3		ENSP00000361978
PKIG	ENST00000372889.5	c.-515-1391T>C		intron_variant		5		ENSP00000361980	P1

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63721 AN: 151970 Hom.: 15672 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.433

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.419 AC: 63727 AN: 152088 Hom.: 15677 Cov.: 32 AF XY: 0.415 AC XY: 30835 AN XY: 74332

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.427

Alfa AF: 0.532 Hom.: 36980

Bravo AF: 0.405

Asia WGS AF: 0.303 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs2027871; hg19: chr20-43209835;