16-57020990-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001384950.1(NLRC5):​c.278C>G​(p.Thr93Ser) 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. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 28)

Consequence

NLRC5
NM_001384950.1 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.509
Variant links:
Genes affected
NLRC5 (HGNC:29933): (NLR family CARD domain containing 5) This gene encodes a member of the caspase recruitment domain-containing NLR family. This gene plays a role in cytokine response and antiviral immunity through its inhibition of NF-kappa-B activation and negative regulation of type I interferon signaling pathways. [provided by RefSeq, Oct 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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=0.059257716).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NLRC5NM_001384950.1 linkuse as main transcriptc.278C>G p.Thr93Ser missense_variant 3/49 ENST00000688547.1 NP_001371879.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NLRC5ENST00000688547.1 linkuse as main transcriptc.278C>G p.Thr93Ser missense_variant 3/49 NM_001384950.1 ENSP00000509992 P2Q86WI3-1

Frequencies

GnomAD3 genomes
Cov.:
28
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
28

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJun 28, 2022The c.278C>G (p.T93S) alteration is located in exon 1 (coding exon 1) of the NLRC5 gene. This alteration results from a C to G substitution at nucleotide position 278, causing the threonine (T) at amino acid position 93 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.57
CADD
Benign
4.4
DANN
Benign
0.95
DEOGEN2
Benign
0.0029
T;T;.
Eigen
Benign
-0.82
Eigen_PC
Benign
-0.82
FATHMM_MKL
Benign
0.12
N
LIST_S2
Benign
0.70
.;T;T
M_CAP
Benign
0.048
D
MetaRNN
Benign
0.059
T;T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
1.8
L;L;L
MutationTaster
Benign
1.0
N;N;N;N
PrimateAI
Benign
0.26
T
PROVEAN
Benign
-0.90
N;N;N
REVEL
Benign
0.039
Sift
Benign
0.56
T;T;T
Sift4G
Uncertain
0.032
D;D;D
Polyphen
0.085
B;B;.
Vest4
0.12
MutPred
0.30
Loss of glycosylation at T93 (P = 0.0613);Loss of glycosylation at T93 (P = 0.0613);Loss of glycosylation at T93 (P = 0.0613);
MVP
0.34
MPC
0.24
ClinPred
0.039
T
GERP RS
1.2
Varity_R
0.023
gMVP
0.18

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.090
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: chr16-57054902; API