chr16-81891527-C-A

Variant names:

• chr16-81891527-C-A
• rs199636472
• NM_002661.5:c.923C>A

Variant summary

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

The NM_002661.5(PLCG2):​c.923C>A​(p.Ala308Glu) 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. A308V) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PLCG2 NM_002661.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.977

Genes affected

PLCG2 (HGNC:9066): (phospholipase C gamma 2) The protein encoded by this gene is a transmembrane signaling enzyme that catalyzes the conversion of 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate to 1D-myo-inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG) using calcium as a cofactor. IP3 and DAG are second messenger molecules important for transmitting signals from growth factor receptors and immune system receptors across the cell membrane. Mutations in this gene have been found in autoinflammation, antibody deficiency, and immune dysregulation syndrome and familial cold autoinflammatory syndrome 3. [provided by RefSeq, Mar 2014]

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=0.036895365).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLCG2	NM_002661.5	c.923C>A	p.Ala308Glu	missense_variant	Exon 11 of 33	ENST00000564138.6	NP_002652.2
PLCG2	NM_001425749.1	c.923C>A	p.Ala308Glu	missense_variant	Exon 12 of 34		NP_001412678.1
PLCG2	NM_001425750.1	c.923C>A	p.Ala308Glu	missense_variant	Exon 11 of 33		NP_001412679.1
PLCG2	NM_001425751.1	c.923C>A	p.Ala308Glu	missense_variant	Exon 12 of 34		NP_001412680.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLCG2	ENST00000564138.6	c.923C>A	p.Ala308Glu	missense_variant	Exon 11 of 33	1	NM_002661.5	ENSP00000482457.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	4.2
DANN	Benign	0.60
DEOGEN2	Benign	0.23	T;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.27	N
LIST_S2	Benign	0.27	T;T
M_CAP	Benign	0.0068	T
MetaRNN	Benign	0.037	T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	-0.88	N;.
PrimateAI	Benign	0.25	T
PROVEAN	Benign	0.78	.;N
REVEL	Benign	0.020
Sift	Benign	0.88	.;T
Sift4G	Benign	1.0	T;T
Polyphen		0.0010	B;.
Vest4		0.19
MutPred		0.40		Gain of disorder (P = 0.0211);Gain of disorder (P = 0.0211);
MVP		0.27
MPC		0.073
ClinPred		0.037	T
GERP RS		0.13
Varity_R		0.042
gMVP		0.63

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

LitVar

Other links and lift over

dbSNP: rs199636472; hg19: chr16-81925132;