chr16-57025557-C-T

Variant summary

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

The NM_001384950.1(NLRC5):​c.614C>T​(p.Ala205Val) 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: 33)

Consequence

NLRC5
NM_001384950.1 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.185
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]

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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=0.04483965).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NLRC5NM_001384950.1 linkuse as main transcriptc.614C>T p.Ala205Val missense_variant 6/49 ENST00000688547.1 NP_001371879.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NLRC5ENST00000688547.1 linkuse as main transcriptc.614C>T p.Ala205Val missense_variant 6/49 NM_001384950.1 ENSP00000509992 P2Q86WI3-1
NLRC5ENST00000262510.10 linkuse as main transcriptc.614C>T p.Ala205Val missense_variant 6/495 ENSP00000262510 P2Q86WI3-1
NLRC5ENST00000539144.5 linkuse as main transcriptc.614C>T p.Ala205Val missense_variant 4/465 ENSP00000441727 A2Q86WI3-4
NLRC5ENST00000539881.5 linkuse as main transcriptc.614C>T p.Ala205Val missense_variant, NMD_transcript_variant 6/252 ENSP00000441679 Q86WI3-3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
34
GnomAD4 genome
Cov.:
33

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 GeneticsSep 13, 2023The c.614C>T (p.A205V) alteration is located in exon 1 (coding exon 1) of the NLRC5 gene. This alteration results from a C to T substitution at nucleotide position 614, causing the alanine (A) at amino acid position 205 to be replaced by a valine (V). 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
0.086
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.50
CADD
Benign
3.4
DANN
Benign
0.099
DEOGEN2
Benign
0.0054
T;T;.
Eigen
Benign
-0.82
Eigen_PC
Benign
-0.86
FATHMM_MKL
Benign
0.12
N
LIST_S2
Benign
0.63
.;T;T
M_CAP
Benign
0.045
D
MetaRNN
Benign
0.045
T;T;T
MetaSVM
Benign
-0.90
T
MutationAssessor
Benign
1.1
L;L;L
MutationTaster
Benign
1.0
N;N;N;N
PrimateAI
Benign
0.24
T
PROVEAN
Benign
-0.45
N;N;N
REVEL
Benign
0.034
Sift
Benign
1.0
T;T;T
Sift4G
Benign
0.16
T;T;T
Polyphen
0.0060
B;B;B
Vest4
0.021
MutPred
0.33
Gain of methylation at K200 (P = 0.1201);Gain of methylation at K200 (P = 0.1201);Gain of methylation at K200 (P = 0.1201);
MVP
0.31
MPC
0.25
ClinPred
0.052
T
GERP RS
2.8
Varity_R
0.027
gMVP
0.18

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-57059469; API