chr3-17011773-C-T

Variant names:

• chr3-17011773-C-T
• NM_001144382.2:c.2427C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4 BP6_Moderate BP7

The NM_001144382.2(PLCL2):​c.2427C>T​(p.Pro809Pro) variant causes a synonymous 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. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PLCL2 NM_001144382.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.449
• Publications: 0 publications found

Genes affected

PLCL2 (HGNC:9064): (phospholipase C like 2) Enables GABA receptor binding activity. Predicted to be involved in negative regulation of cold-induced thermogenesis and phosphatidylinositol-mediated signaling. Predicted to act upstream of or within several processes, including B cell activation; gamma-aminobutyric acid signaling pathway; and negative regulation of B cell receptor signaling pathway. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.246).
• BP6: Variant 3-17011773-C-T is Benign according to our data. Variant chr3-17011773-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3307402.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.449 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001144382.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCL2	NM_001144382.2	MANE Select	c.2427C>T	p.Pro809Pro	synonymous	Exon 2 of 6	NP_001137854.1	Q9UPR0-1
	PLCL2	NM_015184.5		c.2049C>T	p.Pro683Pro	synonymous	Exon 2 of 6	NP_055999.2	Q9UPR0-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCL2	ENST00000615277.5	TSL:1 MANE Select	c.2427C>T	p.Pro809Pro	synonymous	Exon 2 of 6	ENSP00000478458.1	Q9UPR0-1
	PLCL2	ENST00000432376.5	TSL:1	c.2049C>T	p.Pro683Pro	synonymous	Exon 2 of 6	ENSP00000412836.1	Q9UPR0-3
	PLCL2	ENST00000955152.1		c.2427C>T	p.Pro809Pro	synonymous	Exon 2 of 5	ENSP00000625211.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	7.7
DANN	Benign	0.35
PhyloP100		0.45

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

Other links and lift over

hg19: chr3-17053265;