rs7639979

chr3-46733286-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_147121.1(PRSS46P):n.559+350T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,106 control chromosomes in the GnomAD database, including 5,034 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 0.23 (5034 hom., cov: 32)
• Consequence: PRSS46P NR_147121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

PRSS46P (HGNC:37325): (serine protease 46, pseudogene) Predicted to enable serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be active in extracellular space. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRSS46P	NR_147121.1	n.559+350T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRSS46P	ENST00000463091.2	n.561+350T>C		intron_variant, non_coding_transcript_variant		4
PRSS46P	ENST00000645911.2	n.520+350T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34591 AN: 151988 Hom.: 5027 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.228 AC: 34642 AN: 152106 Hom.: 5034 Cov.: 32 AF XY: 0.230 AC XY: 17073 AN XY: 74368

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.211

Alfa AF: 0.168 Hom.: 1331

Bravo AF: 0.237

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.031
Dann	Benign	0.39

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: rs7639979; hg19: chr3-46774776;