rs10511793

chr9-26924623-T-C

Variant summary

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

The NM_001031689.3(PLAA):c.869+1202A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,120 control chromosomes in the GnomAD database, including 4,020 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 0.21 (4020 hom., cov: 32)
• Consequence: PLAA NM_001031689.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

Genes affected

PLAA (HGNC:9043): (phospholipase A2 activating protein) Predicted to enable ubiquitin binding activity. Involved in cellular response to lipopolysaccharide; macroautophagy; and positive regulation of phospholipase A2 activity. Located in cytoplasm; extracellular exosome; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLAA	NM_001031689.3	c.869+1202A>G		intron_variant		ENST00000397292.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLAA	ENST00000397292.8	c.869+1202A>G		intron_variant		1	NM_001031689.3	P1
PLAA	ENST00000520884.5	c.869+1202A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31803 AN: 152002 Hom.: 4004 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0349

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.209 AC: 31862 AN: 152120 Hom.: 4020 Cov.: 32 AF XY: 0.207 AC XY: 15381 AN XY: 74368

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0348

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.223

Alfa AF: 0.179 Hom.: 1260

Bravo AF: 0.214

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	7.7
Dann	Benign	0.82

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: rs10511793; hg19: chr9-26924621;