NM_001377142.1:c.369+3305A>G

Variant names:

• chr20-9342342-A-G
• rs7268671
• NM_001377142.1:c.369+3305A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001377142.1(PLCB4):​c.369+3305A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0754 in 152,204 control chromosomes in the GnomAD database, including 495 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.075 (495 hom., cov: 32)
• Consequence: PLCB4 NM_001377142.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585
• Publications: 2 publications found

Genes affected

PLCB4 (HGNC:9059): (phospholipase C beta 4) The protein encoded by this gene catalyzes the formation of inositol 1,4,5-trisphosphate and diacylglycerol from phosphatidylinositol 4,5-bisphosphate. This reaction uses calcium as a cofactor and plays an important role in the intracellular transduction of many extracellular signals in the retina. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2010]

PLCB4 Gene-Disease associations (from GenCC):

• auriculocondylar syndrome 2

  Inheritance: AD, AR, SD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P, Illumina, Ambry Genetics
• auriculocondylar syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377142.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCB4	NM_001377142.1	MANE Select	c.369+3305A>G		intron	N/A	NP_001364071.1
	PLCB4	NM_001377143.1		c.369+3305A>G		intron	N/A	NP_001364072.1
	PLCB4	NM_000933.4		c.369+3305A>G		intron	N/A	NP_000924.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLCB4	ENST00000378473.9	TSL:1 MANE Select	c.369+3305A>G		intron	N/A	ENSP00000367734.5
	PLCB4	ENST00000278655.9	TSL:1	c.369+3305A>G		intron	N/A	ENSP00000278655.5
	PLCB4	ENST00000685298.1		c.369+3305A>G		intron	N/A	ENSP00000509390.1

Frequencies

GnomAD3 genomes AF: 0.0754 AC: 11466 AN: 152086 Hom.: 496 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0611

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0574

Gnomad FIN AF: 0.0555

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0647

Gnomad OTH AF: 0.0805

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0754 AC: 11471 AN: 152204 Hom.: 495 Cov.: 32 AF XY: 0.0747 AC XY: 5559 AN XY: 74432

African (AFR) AF: 0.112 AC: 4668 AN: 41508

American (AMR) AF: 0.0610 AC: 932 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0564 AC: 272 AN: 4824

European-Finnish (FIN) AF: 0.0555 AC: 589 AN: 10614

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0647 AC: 4400 AN: 68008

Other (OTH) AF: 0.0796 AC: 168 AN: 2110

Alfa AF: 0.0673 Hom.: 257

Bravo AF: 0.0790

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.20
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

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

dbSNP: rs7268671; hg19: chr20-9322989;