rs2015747

Variant names:

• chr11-86792095-C-A
• rs2015747
• NM_001293180.2:c.-14+900C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001293180.2(PRSS23):​c.-14+900C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 152,278 control chromosomes in the GnomAD database, including 489 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 0.076 (489 hom., cov: 32)
• Consequence: PRSS23 NM_001293180.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRSS23	NM_001293180.2	c.-14+900C>A		intron_variant	Intron 1 of 1		NP_001280109.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRSS23	ENST00000527521.1	c.-14+900C>A		intron_variant	Intron 1 of 1	3		ENSP00000435951.1

Frequencies

GnomAD3 genomes AF: 0.0756 AC: 11497 AN: 152160 Hom.: 489 Cov.: 32

Gnomad AFR AF: 0.0854

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0882

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.00865

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0736

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.0755 AC: 11503 AN: 152278 Hom.: 489 Cov.: 32 AF XY: 0.0735 AC XY: 5471 AN XY: 74462

African (AFR) AF: 0.0852 AC: 3539 AN: 41532

American (AMR) AF: 0.0882 AC: 1349 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3470

East Asian (EAS) AF: 0.00886 AC: 46 AN: 5190

South Asian (SAS) AF: 0.0377 AC: 182 AN: 4830

European-Finnish (FIN) AF: 0.0437 AC: 464 AN: 10618

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0736 AC: 5008 AN: 68020

Other (OTH) AF: 0.0965 AC: 204 AN: 2114

Alfa AF: 0.0782 Hom.: 923

Bravo AF: 0.0807

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2015747; hg19: chr11-86503137;