chr6-83519904-C-T

Position:

• chr6-83519904-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRSS35	NM_153362.3	c.-20-3518C>T		intron_variant		ENST00000369700.4	NP_699193.2
PRSS35	NM_001170423.2	c.-125-1631C>T		intron_variant			NP_001163894.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRSS35	ENST00000369700.4	c.-20-3518C>T		intron_variant		1	NM_153362.3	ENSP00000358714.3

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

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.720

Alfa AF: 0.737 Hom.: 6759

Bravo AF: 0.742

Asia WGS AF: 0.800 AC: 2450 AN: 3062

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.59

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: rs1171115; hg19: chr6-84229623;