8-10537385-T-G

Position:

• chr8-10537385-T-G

Variant summary

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

The NM_198464.4(PRSS55):​c.742-1091T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,982 control chromosomes in the GnomAD database, including 27,866 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 0.60 (27866 hom., cov: 32)
• Consequence: PRSS55 NM_198464.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

Genes affected

PRSS55 (HGNC:30824): (serine protease 55) This gene encodes a member of a group of membrane-anchored chymotrypsin (S1)-like serine proteases. The enocoded protein is primarily expressed in the Leydig and Sertoli cells of the testis and may be involved in male fertility. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2010]

PRSS51 (HGNC:37321): (serine protease 51) Predicted to enable serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

PRSS51 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRSS55	NM_198464.4	c.742-1091T>G		intron_variant		ENST00000328655.8	NP_940866.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRSS55	ENST00000328655.8	c.742-1091T>G		intron_variant		1	NM_198464.4	ENSP00000333003.3

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91746 AN: 151864 Hom.: 27833 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.604 AC: 91833 AN: 151982 Hom.: 27866 Cov.: 32 AF XY: 0.607 AC XY: 45063 AN XY: 74266

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.577

Alfa AF: 0.576 Hom.: 7998

Bravo AF: 0.602

Asia WGS AF: 0.682 AC: 2370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.56

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: rs7008087; hg19: chr8-10394895;