chr10-6504109-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006257.5(PRKCQ):​c.379+3327T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,122 control chromosomes in the GnomAD database, including 15,908 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 ( 15908 hom., cov: 32)

Consequence

PRKCQ
NM_006257.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.26
Variant links:
Genes affected
PRKCQ (HGNC:9410): (protein kinase C theta) Protein kinase C (PKC) is a family of serine- and threonine-specific protein kinases that can be activated by calcium and the second messenger diacylglycerol. PKC family members phosphorylate a wide variety of protein targets and are known to be involved in diverse cellular signaling pathways. PKC family members also serve as major receptors for phorbol esters, a class of tumor promoters. Each member of the PKC family has a specific expression profile and is believed to play a distinct role. The protein encoded by this gene is one of the PKC family members. It is a calcium-independent and phospholipid-dependent protein kinase. This kinase is important for T-cell activation. It is required for the activation of the transcription factors NF-kappaB and AP-1, and may link the T cell receptor (TCR) signaling complex to the activation of the transcription factors. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PRKCQNM_006257.5 linkuse as main transcriptc.379+3327T>C intron_variant ENST00000263125.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PRKCQENST00000263125.10 linkuse as main transcriptc.379+3327T>C intron_variant 1 NM_006257.5 P1Q04759-1
PRKCQENST00000397176.6 linkuse as main transcriptc.379+3327T>C intron_variant 5 Q04759-2
PRKCQENST00000539722.5 linkuse as main transcriptc.5-5551T>C intron_variant 2 Q04759-3

Frequencies

GnomAD3 genomes
AF:
0.416
AC:
63271
AN:
152002
Hom.:
15902
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.116
Gnomad AMI
AF:
0.668
Gnomad AMR
AF:
0.586
Gnomad ASJ
AF:
0.447
Gnomad EAS
AF:
0.485
Gnomad SAS
AF:
0.401
Gnomad FIN
AF:
0.499
Gnomad MID
AF:
0.434
Gnomad NFE
AF:
0.538
Gnomad OTH
AF:
0.455
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.416
AC:
63275
AN:
152122
Hom.:
15908
Cov.:
32
AF XY:
0.416
AC XY:
30946
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.116
Gnomad4 AMR
AF:
0.586
Gnomad4 ASJ
AF:
0.447
Gnomad4 EAS
AF:
0.486
Gnomad4 SAS
AF:
0.402
Gnomad4 FIN
AF:
0.499
Gnomad4 NFE
AF:
0.538
Gnomad4 OTH
AF:
0.450
Alfa
AF:
0.501
Hom.:
9932
Bravo
AF:
0.412
Asia WGS
AF:
0.382
AC:
1331
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.15
DANN
Benign
0.66

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11259272; hg19: chr10-6546071; API