6-122576135-C-T

Variant names:

• chr6-122576135-C-T
• rs9398678
• ENST00000392491.6:c.-247-9786C>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001270394.2(PKIB):​c.-287-9786C>T variant causes a intron 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: 31)
• Consequence: PKIB NM_001270394.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173

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]

ENSG00000287258 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PKIB	NM_001270394.2	c.-287-9786C>T		intron_variant	Intron 2 of 7		NP_001257323.1
PKIB	NM_001270393.2	c.-247-9786C>T		intron_variant	Intron 3 of 7		NP_001257322.1
PKIB	NM_181794.3	c.-247-9786C>T		intron_variant	Intron 2 of 6		NP_861459.1
PKIB	XM_047419002.1	c.-4076-5630C>T		intron_variant	Intron 2 of 8		XP_047274958.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKIB	ENST00000392491.6	c.-247-9786C>T		intron_variant	Intron 2 of 6	1		ENSP00000376281.1
PKIB	ENST00000615438.4	c.-287-9786C>T		intron_variant	Intron 2 of 7	5		ENSP00000480824.1
PKIB	ENST00000583007.2	n.180-5630C>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	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

Publications

LitVar

Other links and lift over

dbSNP: rs9398678; hg19: chr6-122897280;