16-15358993-T-C

Variant names:

• chr16-15358993-T-C
• rs4003228
• ENST00000611162.1:n.16T>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS2: High Homozygotes in GnomAdExome4 at 1315 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G10GP		n.15358993T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G10GP	ENST00000611162.1	n.16T>C		non_coding_transcript_exon_variant	Exon 1 of 2	6

Frequencies

GnomAD3 genomes AF: 0.141 AC: 2423 AN: 17158 Hom.: 376 Cov.: 0

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.154 AC: 257 AN: 1674

American (AMR) AF: 0.181 AC: 363 AN: 2002

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 246 AN: 798

East Asian (EAS) AF: 0.0550 AC: 460 AN: 8360

South Asian (SAS) AF: 0.0917 AC: 771 AN: 8404

European-Finnish (FIN) AF: 0.137 AC: 633 AN: 4604

Middle Eastern (MID) AF: 0.253 AC: 45 AN: 178

European-Non Finnish (NFE) AF: 0.168 AC: 4221 AN: 25182

Other (OTH) AF: 0.148 AC: 423 AN: 2850

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.134 AC: 865 AN: 6450

American (AMR) AF: 0.166 AC: 190 AN: 1144

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 89 AN: 250

East Asian (EAS) AF: 0.0292 AC: 29 AN: 994

South Asian (SAS) AF: 0.120 AC: 46 AN: 382

European-Finnish (FIN) AF: 0.119 AC: 119 AN: 1004

Middle Eastern (MID) AF: 0.0500 AC: 1 AN: 20

European-Non Finnish (NFE) AF: 0.154 AC: 1027 AN: 6666

Other (OTH) AF: 0.218 AC: 48 AN: 220

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs4003228; hg19: chr16-15452850;