rs10853869

Positions:

• chr19-54127722-G-A

Variant summary

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

The ENST00000321030.9(PRPF31):​c.946-351G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,936 control chromosomes in the GnomAD database, including 7,646 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 0.31 (7646 hom., cov: 33)
• Consequence: PRPF31 ENST00000321030.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

PRPF31 (HGNC:15446): (pre-mRNA processing factor 31) This gene encodes a component of the spliceosome complex and is one of several retinitis pigmentosa-causing genes. When the gene product is added to the spliceosome complex, activation occurs.[provided by RefSeq, Jan 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRPF31	NM_015629.4	c.946-351G>A		intron_variant		ENST00000321030.9	NP_056444.3
PRPF31	XM_006723137.5	c.946-351G>A		intron_variant			XP_006723200.1
PRPF31	XM_047438587.1	c.974-351G>A		intron_variant			XP_047294543.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRPF31	ENST00000321030.9	c.946-351G>A		intron_variant		1	NM_015629.4	ENSP00000324122	P1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47130 AN: 151820 Hom.: 7625 Cov.: 33

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.0632

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.311 AC: 47190 AN: 151936 Hom.: 7646 Cov.: 33 AF XY: 0.308 AC XY: 22863 AN XY: 74258

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.0632

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.321

Alfa AF: 0.286 Hom.: 7497

Bravo AF: 0.314

Asia WGS AF: 0.229 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.75

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: rs10853869; hg19: chr19-54631097;