rs11539752

Variant names:

• chr14-24632383-G-A
• rs11539752
• NM_004131.6:c.280C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-24632383-G-A
• chr14-24632383-G-C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_004131.6(GZMB):​c.280C>T​(p.Pro94Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. 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. P94A) has been classified as Benign.

• Frequency: Genomes: not found (cov: 30)
• Consequence: GZMB NM_004131.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 0 publications found

Genes affected

GZMB (HGNC:4709): (granzyme B) This gene encodes a member of the granzyme subfamily of proteins, part of the peptidase S1 family of serine proteases. The encoded preproprotein is secreted by natural killer (NK) cells and cytotoxic T lymphocytes (CTLs) and proteolytically processed to generate the active protease, which induces target cell apoptosis. This protein also processes cytokines and degrades extracellular matrix proteins, and these roles are implicated in chronic inflammation and wound healing. Expression of this gene may be elevated in human patients with cardiac fibrosis. [provided by RefSeq, Sep 2016]

ENSG00000258657 (HGNC:58166):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13165197).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GZMB	NM_004131.6	c.280C>T	p.Pro94Ser	missense_variant	Exon 3 of 5	ENST00000216341.9	NP_004122.2
GZMB	NM_001346011.2	c.244C>T	p.Pro82Ser	missense_variant	Exon 3 of 5		NP_001332940.1
GZMB	NR_144343.2	n.234-265C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GZMB	ENST00000216341.9	c.280C>T	p.Pro94Ser	missense_variant	Exon 3 of 5	1	NM_004131.6	ENSP00000216341.4

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	0.37
DANN	Benign	0.62
DEOGEN2	Benign	0.20	.;T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.015	N
LIST_S2	Benign	0.092	T;T
M_CAP	Benign	0.076	D
MetaRNN	Benign	0.13	T;T
MetaSVM	Benign	-0.77	T
MutationAssessor	Benign	-0.64	.;N
PhyloP100		-1.4
PrimateAI	Benign	0.31	T
PROVEAN	Benign	1.0	N;N
REVEL	Benign	0.16
Sift	Benign	0.066	T;T
Sift4G	Benign	0.42	T;T
Polyphen		0.0010	.;B
Vest4		0.058
MutPred		0.45		.;Gain of phosphorylation at P94 (P = 0.0809);
MVP		0.64
MPC		0.18
ClinPred		0.079	T
GERP RS		-0.76
Varity_R		0.11
gMVP		0.65
Mutation Taster		=91/9	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11539752; hg19: chr14-25101589;