dbSNP rs9368492: PRSS16:c.1150+790A>G (chr6-27253739-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005865.4(PRSS16):c.1150+790A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 198,104 control chromosomes in the GnomAD database, including 1,474 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 0.12 ( 1235 hom., cov: 32)

Exomes 𝑓: 0.091 ( 239 hom. )

Consequence

PRSS16
NM_005865.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.361

Publications

2 publications found

Variant links:

Genes affected

PRSS16 (HGNC:9480): (serine protease 16) This gene encodes a serine protease expressed exclusively in the thymus. It is thought to play a role in the alternative antigen presenting pathway used by cortical thymic epithelial cells during the positive selection of T cells. The gene is found in the large histone gene cluster on chromosome 6, near the major histocompatibility complex (MHC) class I region. A second transcript variant has been described, but its full length nature has not been determined. [provided by RefSeq, Jul 2008]

PRSS16 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005865.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRSS16	NM_005865.4	MANE Select	c.1150+790A>G		intron	N/A	NP_005856.1	Q9NQE7
	PRSS16	NM_001438051.1		c.379+790A>G		intron	N/A	NP_001424980.1	F2Z2N5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PRSS16	ENST00000230582.8	TSL:1 MANE Select	c.1150+790A>G	intron	N/A	ENSP00000230582.3	Q9NQE7
PRSS16	ENST00000377456.6	TSL:1	n.454-1247A>G	intron	N/A
PRSS16	ENST00000916331.1		c.859+790A>G	intron	N/A	ENSP00000586390.1

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17909

AN:

152038

Hom.:

1234

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.0879

Gnomad AMR

AF:

0.0820

Gnomad ASJ

AF:

0.0759

Gnomad EAS

AF:

0.116

Gnomad SAS

AF:

0.0774

Gnomad FIN

AF:

0.223

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.103

Gnomad OTH

AF:

0.116

GnomAD4 exome

AF:

0.0909

AC:

4175

AN:

45948

Hom.:

239

Cov.:

AF XY:

0.0865

AC XY:

2124

AN XY:

24560

show subpopulations

African (AFR)

AF:

0.134

AC:

173

AN:

1292

American (AMR)

AF:

0.0644

AC:

195

AN:

3028

Ashkenazi Jewish (ASJ)

AF:

0.0780

AC:

AN:

1090

East Asian (EAS)

AF:

0.0887

AC:

173

AN:

1950

South Asian (SAS)

AF:

0.0631

AC:

451

AN:

7148

European-Finnish (FIN)

AF:

0.160

AC:

366

AN:

2290

Middle Eastern (MID)

AF:

0.0833

AC:

AN:

156

European-Non Finnish (NFE)

AF:

0.0927

AC:

2466

AN:

26592

Other (OTH)

AF:

0.105

AC:

253

AN:

2402

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

189

379

568

758

947

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.118

AC:

17916

AN:

152156

Hom.:

1235

Cov.:

AF XY:

0.122

AC XY:

9078

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.138

AC:

5741

AN:

41496

American (AMR)

AF:

0.0818

AC:

1252

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0759

AC:

263

AN:

3464

East Asian (EAS)

AF:

0.116

AC:

599

AN:

5182

South Asian (SAS)

AF:

0.0781

AC:

377

AN:

4826

European-Finnish (FIN)

AF:

0.223

AC:

2356

AN:

10570

Middle Eastern (MID)

AF:

0.103

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.103

AC:

6973

AN:

68006

Other (OTH)

AF:

0.116

AC:

245

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

795

1590

2384

3179

3974

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

202

404

606

808

1010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.103

Hom.:

384

Bravo

AF:

0.109

Asia WGS

AF:

0.0820

AC:

286

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

7.4

(source)

DANN

Benign

0.62

PhyloP100

-0.36

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over