chr6-83519904-C-T

Variant names:

• chr6-83519904-C-T
• rs1171115
• NM_153362.3:c.-20-3518C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153362.3(PRSS35):​c.-20-3518C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 150,698 control chromosomes in the GnomAD database, including 42,054 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 0.74 (42054 hom., cov: 29)
• Consequence: PRSS35 NM_153362.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 8 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153362.3. 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
	PRSS35	NM_153362.3	MANE Select	c.-20-3518C>T		intron	N/A	NP_699193.2	Q8N3Z0
	PRSS35	NM_001170423.2		c.-125-1631C>T		intron	N/A	NP_001163894.1	Q8N3Z0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRSS35	ENST00000369700.4	TSL:1 MANE Select	c.-20-3518C>T		intron	N/A	ENSP00000358714.3	Q8N3Z0
	PRSS35	ENST00000867649.1		c.-125-1631C>T		intron	N/A	ENSP00000537708.1
	PRSS35	ENST00000867650.1		c.-426-1330C>T		intron	N/A	ENSP00000537709.1

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112072 AN: 150580 Hom.: 42000 Cov.: 29

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.744 AC: 112182 AN: 150698 Hom.: 42054 Cov.: 29 AF XY: 0.749 AC XY: 55127 AN XY: 73600

African (AFR) AF: 0.765 AC: 31154 AN: 40744

American (AMR) AF: 0.777 AC: 11779 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2240 AN: 3454

East Asian (EAS) AF: 0.880 AC: 4505 AN: 5120

South Asian (SAS) AF: 0.836 AC: 3953 AN: 4728

European-Finnish (FIN) AF: 0.752 AC: 7877 AN: 10480

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.715 AC: 48429 AN: 67724

Other (OTH) AF: 0.720 AC: 1503 AN: 2088

Alfa AF: 0.737 Hom.: 6969

Bravo AF: 0.742

Asia WGS AF: 0.800 AC: 2450 AN: 3062

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.59
PhyloP100		-0.59
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: rs1171115; hg19: chr6-84229623;