rs4003228

chr16-15358993-T-C

Variant summary

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

The ENST00000611162.1(PLA2G10GP):n.16T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.14 (376 hom., cov: 0)
  • Exomes 𝑓: 0.14 (1315 hom.)
  • Failed GnomAD Quality Control
• Consequence: PLA2G10GP ENST00000611162.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

Genes affected

PLA2G10GP (HGNC:56603): (phospholipase A2 group XG, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G10GP	ENST00000611162.1	n.16T>C		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2423 AN: 17158 Hom.: 376 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.0292

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0500

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.233

GnomAD4 exome AF: 0.137 AC: 7419 AN: 54052 Hom.: 1315 Cov.: 0 AF XY: 0.137 AC XY: 4022 AN XY: 29346

Gnomad4 AFR exome AF: 0.154

Gnomad4 AMR exome AF: 0.181

Gnomad4 ASJ exome AF: 0.308

Gnomad4 EAS exome AF: 0.0550

Gnomad4 SAS exome AF: 0.0917

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.168

Gnomad4 OTH exome AF: 0.148

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.141 AC: 2423 AN: 17196 Hom.: 376 Cov.: 0 AF XY: 0.142 AC XY: 1165 AN XY: 8220

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.0292

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.218

Alfa AF: 0.211 Hom.: 438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	15
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4003228; hg19: chr16-15452850;