rs12746918

Variant names:

• chr1-2416027-C-T
• rs12746918
• XM_047435029.1:c.-178+15C>T

Variant summary

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

The XM_047435029.1(PLCH2):​c.-178+15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,184 control chromosomes in the GnomAD database, including 3,389 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 0.20 (3389 hom., cov: 33)
• Consequence: PLCH2 XM_047435029.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 7 publications found

Genes affected

PLCH2 (HGNC:29037): (phospholipase C eta 2) PLCH2 is a member of the PLC-eta family of the phosphoinositide-specific phospholipase C (PLC) superfamily of enzymes that cleave PtdIns(4,5) P2 to generate second messengers inositol 1,4,5-trisphosphate and diacylglycerol (Zhou et al., 2005 [PubMed 16107206]).[supplied by OMIM, Jun 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30404 AN: 152066 Hom.: 3381 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.200 AC: 30435 AN: 152184 Hom.: 3389 Cov.: 33 AF XY: 0.207 AC XY: 15386 AN XY: 74416

African (AFR) AF: 0.152 AC: 6309 AN: 41536

American (AMR) AF: 0.305 AC: 4661 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0758 AC: 263 AN: 3470

East Asian (EAS) AF: 0.152 AC: 786 AN: 5168

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4826

European-Finnish (FIN) AF: 0.311 AC: 3297 AN: 10598

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

European-Non Finnish (NFE) AF: 0.200 AC: 13581 AN: 67984

Other (OTH) AF: 0.185 AC: 390 AN: 2110

Alfa AF: 0.216 Hom.: 487

Bravo AF: 0.193

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.84
DANN	Benign	0.53
PhyloP100		-1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12746918; hg19: chr1-2347466;