19-54941461-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001127255.2(NLRP7):​c.251G>C​(p.Cys84Ser) 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. 16/21 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 Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: NLRP7 NM_001127255.2 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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.04402408).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NLRP7	NM_001127255.2	c.251G>C	p.Cys84Ser	missense_variant	Exon 2 of 11		NP_001120727.1
NLRP7	NM_001405531.1	c.251G>C	p.Cys84Ser	missense_variant	Exon 4 of 13		NP_001392460.1
NLRP7	NM_139176.4	c.251G>C	p.Cys84Ser	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>C	p.Cys84Ser	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	0.12
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.69
CADD	Benign	0.25
DANN	Benign	0.17
DEOGEN2	Benign	0.12	T;.;T;.;.;.
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.00039	N
M_CAP	Benign	0.00074	T
MetaRNN	Benign	0.044	T;T;T;T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	-0.39	N;N;N;N;N;.
PrimateAI	Benign	0.41	T
PROVEAN	Benign	-1.6	N;N;.;.;.;.
REVEL	Benign	0.070
Sift	Benign	0.83	T;T;.;.;.;.
Sift4G	Benign	1.0	T;T;T;T;T;.
Polyphen		0.0050	B;B;B;.;.;.
Vest4		0.062
MVP		0.22
MPC		0.30
ClinPred		0.040	T
GERP RS		0.24
Varity_R		0.050
gMVP		0.79

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;