6-122638360-G-C

Position:

• chr6-122638360-G-C

Variant summary

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

The NM_181795.3(PKIB):​c.-76+4993G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,064 control chromosomes in the GnomAD database, including 5,477 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 0.26 (5477 hom., cov: 32)
• Consequence: PKIB NM_181795.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

Genes affected

PKIB (HGNC:9018): (cAMP-dependent protein kinase inhibitor beta) This gene encodes a member of the cAMP-dependent protein kinase inhibitor family. The encoded protein may play a role in the protein kinase A (PKA) pathway by interacting with the catalytic subunit of PKA, and overexpression of this gene may play a role in prostate cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PKIB	NM_181795.3	c.-76+4993G>C		intron_variant		ENST00000368452.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKIB	ENST00000368452.7	c.-76+4993G>C		intron_variant		1	NM_181795.3	P1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38897 AN: 151946 Hom.: 5476 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.256 AC: 38908 AN: 152064 Hom.: 5477 Cov.: 32 AF XY: 0.256 AC XY: 19060 AN XY: 74334

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.239

Alfa AF: 0.172 Hom.: 386

Bravo AF: 0.250

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
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: rs17084680; hg19: chr6-122959505; COSMIC: COSV63761423;