Genetic Variant PRP4K:c.2582-110T>G (chr6-4056926-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003913.5(PRP4K):c.2582-110T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 1,159,616 control chromosomes in the GnomAD database, including 276,630 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 0.71 ( 38147 hom., cov: 33)

Exomes 𝑓: 0.69 ( 238483 hom. )

Consequence

PRP4K
NM_003913.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.114

Publications

7 publications found

Variant links:

Genes affected

PRP4K (HGNC:17346): (pre-mRNA processing factor kinase PRP4K) Pre-mRNA splicing occurs in two sequential transesterification steps, and the protein encoded by this gene is thought to be involved in pre-mRNA splicing and in signal transduction. This protein belongs to a kinase family that includes serine/arginine-rich protein-specific kinases and cyclin-dependent kinases (CDKs). This protein is regarded as a CDK-like kinase (Clk) with homology to mitogen-activated protein kinases (MAPKs). [provided by RefSeq, Jul 2008]

PRP4K links:

FAM217A (HGNC:21362): (family with sequence similarity 217 member A)

FAM217A links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRP4K	NM_003913.5 link	c.2582-110T>G		intron_variant	Intron 12 of 14	ENST00000337659.11	NP_003904.3	Q13523A0A024QZY5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRP4K	ENST00000337659.11 link	c.2582-110T>G		intron_variant	Intron 12 of 14	1	NM_003913.5	ENSP00000337194.6		Q13523

Frequencies

GnomAD3 genomes

AF:

0.707

AC:

107540

AN:

152026

Hom.:

38108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.745

Gnomad AMI

AF:

0.727

Gnomad AMR

AF:

0.733

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.772

Gnomad SAS

AF:

0.673

Gnomad FIN

AF:

0.682

Gnomad MID

AF:

0.665

Gnomad NFE

AF:

0.682

Gnomad OTH

AF:

0.703

GnomAD4 exome

AF:

0.687

AC:

692387

AN:

1007472

Hom.:

238483

Cov.:

AF XY:

0.686

AC XY:

346058

AN XY:

504716

show subpopulations

African (AFR)

AF:

0.739

AC:

17079

AN:

23126

American (AMR)

AF:

0.738

AC:

17245

AN:

23354

Ashkenazi Jewish (ASJ)

AF:

0.682

AC:

11848

AN:

17384

East Asian (EAS)

AF:

0.789

AC:

28750

AN:

36452

South Asian (SAS)

AF:

0.674

AC:

39775

AN:

59018

European-Finnish (FIN)

AF:

0.694

AC:

28094

AN:

40456

Middle Eastern (MID)

AF:

0.671

AC:

2018

AN:

3006

European-Non Finnish (NFE)

AF:

0.680

AC:

517078

AN:

760464

Other (OTH)

AF:

0.690

AC:

30500

AN:

44212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

10223

20446

30670

40893

51116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12110

24220

36330

48440

60550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.707

AC:

107641

AN:

152144

Hom.:

38147

Cov.:

AF XY:

0.707

AC XY:

52558

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.745

AC:

30909

AN:

41500

American (AMR)

AF:

0.733

AC:

11209

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.669

AC:

2321

AN:

3470

East Asian (EAS)

AF:

0.773

AC:

4000

AN:

5174

South Asian (SAS)

AF:

0.672

AC:

3240

AN:

4818

European-Finnish (FIN)

AF:

0.682

AC:

7213

AN:

10582

Middle Eastern (MID)

AF:

0.667

AC:

196

AN:

294

European-Non Finnish (NFE)

AF:

0.682

AC:

46401

AN:

67994

Other (OTH)

AF:

0.704

AC:

1490

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1666

3332

4999

6665

8331

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

840

1680

2520

3360

4200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.699

Hom.:

4616

Bravo

AF:

0.712

Asia WGS

AF:

0.752

AC:

2616

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.4

(source)

DANN

Benign

0.65

PhyloP100

-0.11

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over