rs4806711

Variant names:

• chr19-54115811-G-A
• rs4806711
• NM_015629.4:c.-9+14G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-54115811-G-A
• chr19-54115811-G-C

Variant summary

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

The NM_015629.4(PRPF31):​c.-9+14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 219,942 control chromosomes in the GnomAD database, including 73,513 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 0.82 (51693 hom., cov: 33)
  • Exomes 𝑓: 0.80 (21820 hom.)
• Consequence: PRPF31 NM_015629.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

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]

TFPT (HGNC:13630): (TCF3 fusion partner) Predicted to enable DNA binding activity and protein kinase binding activity. Involved in apoptotic signaling pathway. Located in nucleoplasm. Part of Ino80 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRPF31	NM_015629.4	c.-9+14G>A		intron_variant	Intron 1 of 13	ENST00000321030.9	NP_056444.3
PRPF31	XM_006723137.5	c.-39+14G>A		intron_variant	Intron 1 of 13		XP_006723200.1
PRPF31	XM_047438587.1	c.-9+14G>A		intron_variant	Intron 1 of 9		XP_047294543.1
TFPT	NM_013342.4	c.-542C>T		upstream_gene_variant		ENST00000391759.6	NP_037474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRPF31	ENST00000321030.9	c.-9+14G>A		intron_variant	Intron 1 of 13	1	NM_015629.4	ENSP00000324122.4
TFPT	ENST00000391759.6	c.-542C>T		upstream_gene_variant		1	NM_013342.4	ENSP00000375639.1

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125155 AN: 152070 Hom.: 51637 Cov.: 33

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.821

GnomAD4 exome AF: 0.802 AC: 54317 AN: 67754 Hom.: 21820 Cov.: 0 AF XY: 0.802 AC XY: 25751 AN XY: 32098

Gnomad4 AFR exome AF: 0.886

Gnomad4 AMR exome AF: 0.769

Gnomad4 ASJ exome AF: 0.772

Gnomad4 EAS exome AF: 0.772

Gnomad4 SAS exome AF: 0.793

Gnomad4 FIN exome AF: 0.753

Gnomad4 NFE exome AF: 0.807

Gnomad4 OTH exome AF: 0.809

GnomAD4 genome AF: 0.823 AC: 125269 AN: 152188 Hom.: 51693 Cov.: 33 AF XY: 0.819 AC XY: 60923 AN XY: 74400

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.823

Alfa AF: 0.806 Hom.: 27488

Bravo AF: 0.824

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4806711; hg19: chr19-54619191;