rs4144615

Positions:

• chr11-86941819-G-A
• chr11-86941819-G-T

Variant summary

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

The ENST00000532234.5(PRSS23):​c.*64+2693G>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,996 control chromosomes in the GnomAD database, including 23,674 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 0.55 (23674 hom., cov: 31)
• Consequence: PRSS23 ENST00000532234.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

Genes affected

PRSS23 (HGNC:14370): (serine protease 23) This gene encodes a conserved member of the trypsin family of serine proteases. Mouse studies found a decrease of mRNA levels of this gene after ovulation was induced. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRSS23	NR_120591.3	n.434+2693G>A		intron_variant, non_coding_transcript_variant
PRSS23	NR_120592.2	n.328-9397G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRSS23	ENST00000532234.5	c.*64+2693G>A		intron_variant, NMD_transcript_variant		1
PRSS23	ENST00000533902.2	c.207-9397G>A		intron_variant		4
PRSS23	ENST00000528769.5	n.128+906G>A		intron_variant, non_coding_transcript_variant		2
PRSS23	ENST00000531521.1	n.242+792G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83912 AN: 151878 Hom.: 23670 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.552 AC: 83939 AN: 151996 Hom.: 23674 Cov.: 31 AF XY: 0.550 AC XY: 40835 AN XY: 74312

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.577

Alfa AF: 0.477 Hom.: 1459

Bravo AF: 0.550

Asia WGS AF: 0.465 AC: 1618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4144615; hg19: chr11-86652861;