rs6601481

Variant names:

• chr8-10531972-C-A
• rs6601481
• NM_198464.4:c.598+427C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-10531972-C-A
• chr8-10531972-C-T

Variant summary

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

The NM_198464.4(PRSS55):​c.598+427C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,996 control chromosomes in the GnomAD database, including 28,195 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 0.61 (28195 hom., cov: 33)
• Consequence: PRSS55 NM_198464.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 2 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRSS55	NM_198464.4	c.598+427C>A		intron_variant	Intron 3 of 4	ENST00000328655.8	NP_940866.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRSS55	ENST00000328655.8	c.598+427C>A		intron_variant	Intron 3 of 4	1	NM_198464.4	ENSP00000333003.3

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92031 AN: 151878 Hom.: 28137 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.606 AC: 92153 AN: 151996 Hom.: 28195 Cov.: 33 AF XY: 0.610 AC XY: 45299 AN XY: 74288

African (AFR) AF: 0.529 AC: 21891 AN: 41420

American (AMR) AF: 0.630 AC: 9620 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1796 AN: 3470

East Asian (EAS) AF: 0.753 AC: 3884 AN: 5160

South Asian (SAS) AF: 0.697 AC: 3355 AN: 4812

European-Finnish (FIN) AF: 0.638 AC: 6744 AN: 10572

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43174 AN: 67974

Other (OTH) AF: 0.575 AC: 1213 AN: 2108

Alfa AF: 0.542 Hom.: 2600

Bravo AF: 0.597

Asia WGS AF: 0.701 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.81
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6601481; hg19: chr8-10389482;