NM_001008270.3:c.643G>T

Variant names:

• chr7-141836460-C-A
• rs745313899
• NM_001008270.3:c.643G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001008270.3(PRSS37):​c.643G>T​(p.Val215Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V215I) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PRSS37 NM_001008270.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.60
• Publications: 0 publications found

Genes affected

PRSS37 (HGNC:29211): (serine protease 37) Predicted to enable serine-type endopeptidase activity. Involved in positive regulation of acrosome reaction and regulation of protein processing. Located in acrosomal vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001008270.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRSS37	NM_001008270.3	MANE Select	c.643G>T	p.Val215Phe	missense	Exon 5 of 5	NP_001008271.2
	PRSS37	NM_001370403.1		c.643G>T	p.Val215Phe	missense	Exon 6 of 6	NP_001357332.1
	PRSS37	NM_001171951.2		c.640G>T	p.Val214Phe	missense	Exon 5 of 5	NP_001165422.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRSS37	ENST00000350549.8	TSL:1 MANE Select	c.643G>T	p.Val215Phe	missense	Exon 5 of 5	ENSP00000297767.3
	PRSS37	ENST00000452758.1	TSL:1	n.*413G>T		non_coding_transcript_exon	Exon 5 of 5	ENSP00000395287.1
	PRSS37	ENST00000452758.1	TSL:1	n.*413G>T		3_prime_UTR	Exon 5 of 5	ENSP00000395287.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.41
BayesDel_addAF	Pathogenic	0.19	D
BayesDel_noAF	Uncertain	0.040
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.40	T
Eigen	Uncertain	0.48
Eigen_PC	Uncertain	0.40
FATHMM_MKL	Benign	0.71	D
LIST_S2	Benign	0.79	T
M_CAP	Uncertain	0.13	D
MetaRNN	Uncertain	0.67	D
MetaSVM	Uncertain	-0.025	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		3.6
PrimateAI	Benign	0.41	T
PROVEAN	Uncertain	-2.7	D
REVEL	Uncertain	0.54
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.014	D
Polyphen		0.99	D
Vest4		0.47
MutPred		0.66		Loss of sheet (P = 0.1158)
MVP		0.91
MPC		0.63
ClinPred		0.94	D
GERP RS		4.3
Varity_R		0.35
gMVP		0.37
Mutation Taster		=79/21	polymorphism

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: rs745313899; hg19: chr7-141536260;