1-227818357-C-T

Variant names:

• chr1-227818357-C-T
• rs4128390
• NM_183062.3:c.583+877C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_183062.3(PRSS38):​c.583+877C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,040 control chromosomes in the GnomAD database, including 27,057 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 0.58 (27057 hom., cov: 32)
• Consequence: PRSS38 NM_183062.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 1 publications found

Genes affected

PRSS38 (HGNC:29625): (serine protease 38) 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRSS38	NM_183062.3	c.583+877C>T		intron_variant	Intron 3 of 4	ENST00000366757.4	NP_898885.1
PRSS38	NM_001374657.2	c.583+877C>T		intron_variant	Intron 3 of 3		NP_001361586.1
PRSS38	XM_011544175.3	c.583+877C>T		intron_variant	Intron 3 of 4		XP_011542477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRSS38	ENST00000366757.4	c.583+877C>T		intron_variant	Intron 3 of 4	1	NM_183062.3	ENSP00000355719.3

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87694 AN: 151922 Hom.: 27019 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.577 AC: 87788 AN: 152040 Hom.: 27057 Cov.: 32 AF XY: 0.582 AC XY: 43228 AN XY: 74310

African (AFR) AF: 0.794 AC: 32947 AN: 41484

American (AMR) AF: 0.576 AC: 8804 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1562 AN: 3468

East Asian (EAS) AF: 0.734 AC: 3805 AN: 5182

South Asian (SAS) AF: 0.521 AC: 2506 AN: 4814

European-Finnish (FIN) AF: 0.527 AC: 5568 AN: 10564

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30923 AN: 67936

Other (OTH) AF: 0.564 AC: 1192 AN: 2112

Alfa AF: 0.482 Hom.: 9121

Bravo AF: 0.591

Asia WGS AF: 0.615 AC: 2140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	11
DANN	Benign	0.93
PhyloP100		-0.16
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: rs4128390; hg19: chr1-228006058;