chr16-31089829-T-G

Variant names:

• chr16-31089829-T-G
• rs17878521
• ENST00000529564.1:c.284-2003A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000529564.1(ENSG00000255439):​c.284-2003A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0152 in 152,124 control chromosomes in the GnomAD database, including 60 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 0.015 (60 hom., cov: 32)
• Consequence: ENSG00000255439 ENST00000529564.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524

Genes affected

ENSG00000255439 (HGNC:):

PRSS53 (HGNC:34407): (serine protease 53) 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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0152 (2319/152124) while in subpopulation AFR AF= 0.0486 (2016/41482). AF 95% confidence interval is 0.0468. There are 60 homozygotes in gnomad4. There are 1089 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 60 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255439	ENST00000529564.1	c.284-2003A>C		intron_variant	Intron 2 of 4	4		ENSP00000431371.1
ENSG00000255439	ENST00000533518.5	n.*42+1263A>C		intron_variant	Intron 3 of 12	1		ENSP00000433035.1
ENSG00000255439	ENST00000532364.1	c.174-2931A>C		intron_variant	Intron 1 of 1	4		ENSP00000460316.1
PRSS53	ENST00000486499.1	n.-201A>C		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.0152 AC: 2314 AN: 152006 Hom.: 60 Cov.: 32

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00577

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000750

Gnomad OTH AF: 0.00956

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

GnomAD4 genome AF: 0.0152 AC: 2319 AN: 152124 Hom.: 60 Cov.: 32 AF XY: 0.0146 AC XY: 1089 AN XY: 74360

Gnomad4 AFR AF: 0.0486

Gnomad4 AMR AF: 0.00570

Gnomad4 ASJ AF: 0.0392

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000750

Gnomad4 OTH AF: 0.00946

Alfa AF: 0.0142 Hom.: 8

Bravo AF: 0.0174

Asia WGS AF: 0.00318 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.73

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: rs17878521; hg19: chr16-31101150;