rs10733604

Positions:

• chr9-113279983-A-C
• chr9-113279983-A-G
• chr9-113279983-A-T

Variant summary

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

The NM_001244926.2(PRPF4):​c.392+852A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 152,094 control chromosomes in the GnomAD database, including 58,689 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 0.88 (58689 hom., cov: 30)
• Consequence: PRPF4 NM_001244926.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

Genes affected

PRPF4 (HGNC:17349): (pre-mRNA splicing tri-snRNP complex factor PRPF4) The protein encoded by this gene is part of a heteromeric complex that binds U4, U5, and U6 small nuclear RNAs and is involved in pre-mRNA splicing. The encoded protein also is a mitotic checkpoint protein and a regulator of chemoresistance in human ovarian cancer. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRPF4	NM_001244926.2	c.392+852A>C		intron_variant		ENST00000374198.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRPF4	ENST00000374198.5	c.392+852A>C		intron_variant		1	NM_001244926.2	A1
PRPF4	ENST00000374199.9	c.395+852A>C		intron_variant		1		P4
PRPF4	ENST00000488937.1	n.36+852A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133350 AN: 151976 Hom.: 58637 Cov.: 30

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.878 AC: 133463 AN: 152094 Hom.: 58689 Cov.: 30 AF XY: 0.875 AC XY: 65040 AN XY: 74334

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.892

Alfa AF: 0.873 Hom.: 73551

Bravo AF: 0.883

Asia WGS AF: 0.953 AC: 3316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.64

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: rs10733604; hg19: chr9-116042263;