chr1-56637546-A-G

Variant names:

• chr1-56637546-A-G
• rs11206883
• ENST00000461655.1:n.241+5922T>C

Variant summary

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

The ENST00000476206.1(PLPP3):​n.180+5954T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,144 control chromosomes in the GnomAD database, including 52,728 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 0.83 (52728 hom., cov: 32)
• Consequence: PLPP3 ENST00000476206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 4 publications found

Genes affected

PLPP3 (HGNC:9229): (phospholipid phosphatase 3) The protein encoded by this gene is a member of the phosphatidic acid phosphatase (PAP) family. PAPs convert phosphatidic acid to diacylglycerol, and function in de novo synthesis of glycerolipids as well as in receptor-activated signal transduction mediated by phospholipase D. This protein is a membrane glycoprotein localized at the cell plasma membrane. It has been shown to actively hydrolyze extracellular lysophosphatidic acid and short-chain phosphatidic acid. The expression of this gene is found to be enhanced by epidermal growth factor in Hela cells. [provided by RefSeq, Mar 2010]

LOC101929935 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000476206.1. 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
	LOC101929935	NR_135111.1		n.226+5954T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLPP3	ENST00000461655.1	TSL:3	n.241+5922T>C		intron	N/A
	PLPP3	ENST00000476206.1	TSL:2	n.180+5954T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125889 AN: 152026 Hom.: 52699 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.828 AC: 125970 AN: 152144 Hom.: 52728 Cov.: 32 AF XY: 0.825 AC XY: 61348 AN XY: 74364

African (AFR) AF: 0.727 AC: 30154 AN: 41466

American (AMR) AF: 0.862 AC: 13180 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3071 AN: 3470

East Asian (EAS) AF: 0.709 AC: 3659 AN: 5160

South Asian (SAS) AF: 0.634 AC: 3057 AN: 4824

European-Finnish (FIN) AF: 0.908 AC: 9616 AN: 10590

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60437 AN: 68026

Other (OTH) AF: 0.834 AC: 1765 AN: 2116

Alfa AF: 0.865 Hom.: 91742

Bravo AF: 0.824

Asia WGS AF: 0.701 AC: 2440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.056
DANN	Benign	0.78
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11206883; hg19: chr1-57103219;