rs7268671

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLCB4	NM_001377142.1	c.369+3305A>G		intron_variant	Intron 7 of 39	ENST00000378473.9	NP_001364071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLCB4	ENST00000378473.9	c.369+3305A>G		intron_variant	Intron 7 of 39	1	NM_001377142.1	ENSP00000367734.5

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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0610

Gnomad4 ASJ AF: 0.0974

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0564

Gnomad4 FIN AF: 0.0555

Gnomad4 NFE AF: 0.0647

Gnomad4 OTH AF: 0.0796

Alfa AF: 0.0673 Hom.: 179

Bravo AF: 0.0790

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.20

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: rs7268671; hg19: chr20-9322989;