chr16-15358993-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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611162.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G10GP	ENST00000611162.1	TSL:6	n.16T>C		non_coding_transcript_exon	Exon 1 of 2

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4003228;

hg19: chr16-15452850;