Variant rs3812141 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_153362.3(PRSS35):c.984C>T(p.Ser328Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,613,828 control chromosomes in the GnomAD database, including 23,057 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 0.18 ( 2691 hom., cov: 32)

Exomes 𝑓: 0.16 ( 20366 hom. )

Consequence

PRSS35
NM_153362.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.34

Variant links:

Genes affected

PRSS35 (HGNC:21387): (serine protease 35) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

PRSS35 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP7

Synonymous conserved (PhyloP=-3.34 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRSS35	NM_153362.3 link	c.984C>T	p.Ser328Ser	synonymous_variant	2/2	ENST00000369700.4	NP_699193.2	Q8N3Z0
PRSS35	NM_001170423.2 link	c.984C>T	p.Ser328Ser	synonymous_variant	3/3		NP_001163894.1	Q8N3Z0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRSS35	ENST00000369700.4 link	c.984C>T	p.Ser328Ser	synonymous_variant	2/2	1	NM_153362.3	ENSP00000358714.3		Q8N3Z0

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27278

AN:

151848

Hom.:

2689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.247

Gnomad AMI

AF:

0.194

Gnomad AMR

AF:

0.121

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.238

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.144

Gnomad MID

AF:

0.160

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.168

GnomAD3 exomes

AF:

0.168

AC:

42173

AN:

250956

Hom.:

3972

AF XY:

0.173

AC XY:

23446

AN XY:

135676

show subpopulations

Gnomad AFR exome

AF:

0.244

Gnomad AMR exome

AF:

0.0843

Gnomad ASJ exome

AF:

0.166

Gnomad EAS exome

AF:

0.260

Gnomad SAS exome

AF:

0.238

Gnomad FIN exome

AF:

0.148

Gnomad NFE exome

AF:

0.154

Gnomad OTH exome

AF:

0.157

GnomAD4 exome

AF:

0.163

AC:

237954

AN:

1461862

Hom.:

20366

Cov.:

AF XY:

0.165

AC XY:

120353

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.251

Gnomad4 AMR exome

AF:

0.0877

Gnomad4 ASJ exome

AF:

0.165

Gnomad4 EAS exome

AF:

0.270

Gnomad4 SAS exome

AF:

0.238

Gnomad4 FIN exome

AF:

0.154

Gnomad4 NFE exome

AF:

0.154

Gnomad4 OTH exome

AF:

0.166

GnomAD4 genome

AF:

0.180

AC:

27282

AN:

151966

Hom.:

2691

Cov.:

AF XY:

0.181

AC XY:

13473

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.247

Gnomad4 AMR

AF:

0.121

Gnomad4 ASJ

AF:

0.160

Gnomad4 EAS

AF:

0.238

Gnomad4 SAS

AF:

0.234

Gnomad4 FIN

AF:

0.144

Gnomad4 NFE

AF:

0.150

Gnomad4 OTH

AF:

0.167

Alfa

AF:

0.158

Hom.:

3389

Bravo

AF:

0.177

Asia WGS

AF:

0.180

AC:

623

AN:

3478

EpiCase

AF:

0.151

EpiControl

AF:

0.149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

0.22

DANN

Benign

0.75

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over