rs853406

Variant names:

• chr6-4056926-T-A
• rs853406
• NM_003913.5:c.2582-110T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-4056926-T-A
• chr6-4056926-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003913.5(PRP4K):​c.2582-110T>A 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PRP4K NM_003913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 7 publications found

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]

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1009874 Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0 AN XY: 505904

African (AFR) AF: 0.00 AC: 0 AN: 23164

American (AMR) AF: 0.00 AC: 0 AN: 23396

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17412

East Asian (EAS) AF: 0.00 AC: 0 AN: 36500

South Asian (SAS) AF: 0.00 AC: 0 AN: 59126

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40552

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3012

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 762408

Other (OTH) AF: 0.00 AC: 0 AN: 44304

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		-0.11

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

Other links and lift over

dbSNP: rs853406; hg19: chr6-4057160;