chr1-56637546-A-G

Position:

• chr1-56637546-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_135111.1(LOC101929935):​n.226+5954T>C variant causes a intron, non coding transcript 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: LOC101929935 NR_135111.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

LOC101929935 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929935	NR_135111.1	n.226+5954T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLPP3	ENST00000461655.1	n.241+5922T>C		intron_variant, non_coding_transcript_variant		3
PLPP3	ENST00000476206.1	n.180+5954T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.885

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.834

Alfa AF: 0.869 Hom.: 71846

Bravo AF: 0.824

Asia WGS AF: 0.701 AC: 2440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11206883; hg19: chr1-57103219;