ENST00000588756.5:c.251G>T

Variant names:

• chr19-54941461-C-A
• ENST00000588756.5:c.251G>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000588756.5(NLRP7):​c.251G>T​(p.Cys84Phe) 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. 15/21 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. C84Y) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: NLRP7 ENST00000588756.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373

Genes affected

NLRP7 (HGNC:22947): (NLR family pyrin domain containing 7) This gene encodes a member of the NACHT, leucine rich repeat, and PYD containing (NLRP) protein family. It has an N-terminal pyrin domain, followed by a NACHT domain, a NACHT-associated domain (NAD), and a C-terminal leucine-rich repeat (LRR) region. NLRP proteins are implicated in the activation of proinflammatory caspases through multiprotein complexes called inflammasomes. This gene may act as a feedback regulator of caspase-1-dependent interleukin 1-beta secretion. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.108341515).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NLRP7	NM_001127255.2	c.251G>T	p.Cys84Phe	missense_variant	Exon 2 of 11		NP_001120727.1
NLRP7	NM_001405531.1	c.251G>T	p.Cys84Phe	missense_variant	Exon 4 of 13		NP_001392460.1
NLRP7	NM_139176.4	c.251G>T	p.Cys84Phe	missense_variant	Exon 2 of 11		NP_631915.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NLRP7	ENST00000592784.6	c.251G>T	p.Cys84Phe	missense_variant	Exon 2 of 11	1		ENSP00000468706.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	11
DANN	Benign	0.83
DEOGEN2	Benign	0.16	T;.;T;.;.;.
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.0031	N
M_CAP	Benign	0.0022	T
MetaRNN	Benign	0.11	T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.7	L;L;L;L;L;.
PrimateAI	Benign	0.42	T
PROVEAN	Uncertain	-3.1	D;D;.;.;.;.
REVEL	Benign	0.089
Sift	Uncertain	0.0060	D;D;.;.;.;.
Sift4G	Uncertain	0.033	D;D;D;D;D;.
Polyphen		0.59	P;B;P;.;.;.
Vest4		0.20
MVP		0.38
MPC		0.47
ClinPred		0.29	T
GERP RS		0.24
Varity_R		0.22
gMVP		0.85

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-55452829;