rs244128

Variant names:

• chr20-44540989-G-C
• rs244128
• ENST00000372894.7:c.-94+9011G>C

Variant summary

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

The NM_007066.5(PKIG):​c.-94+9011G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,100 control chromosomes in the GnomAD database, including 15,523 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 0.41 (15523 hom., cov: 32)
• Consequence: PKIG NM_007066.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.842

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=-0.86).
• 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 rank	MANE	Protein	UniProt
PKIG	NM_001281444.2	c.-516+9011G>C		intron_variant	Intron 1 of 5		NP_001268373.1
PKIG	NM_007066.5	c.-94+9011G>C		intron_variant	Intron 1 of 3		NP_008997.1
PKIG	NM_181804.3	c.-241+9011G>C		intron_variant	Intron 1 of 4		NP_861520.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKIG	ENST00000372894.7	c.-94+9011G>C		intron_variant	Intron 1 of 3	1		ENSP00000361985.3
PKIG	ENST00000372889.5	c.-516+9011G>C		intron_variant	Intron 1 of 5	5		ENSP00000361980.1
PKIG	ENST00000372891.7	c.-346+9011G>C		intron_variant	Intron 1 of 5	2		ENSP00000361981.3

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62738 AN: 151982 Hom.: 15518 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.413 AC: 62746 AN: 152100 Hom.: 15523 Cov.: 32 AF XY: 0.409 AC XY: 30407 AN XY: 74336

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.421

Alfa AF: 0.477 Hom.: 2400

Bravo AF: 0.398

Asia WGS AF: 0.305 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.65

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: rs244128; hg19: chr20-43169630;