rs12192877

chr6-36675222-C-Achr6-36675222-C-G

Variant summary

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

The ENST00000454686.1(LAP3P2):n.1406C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,514,914 control chromosomes in the GnomAD database, including 24,263 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 0.22 (4461 hom., cov: 32)
  • Exomes 𝑓: 0.15 (19802 hom.)
• Consequence: LAP3P2 ENST00000454686.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.91

Genes affected

LAP3P2 (HGNC:42365): (leucine aminopeptidase 3 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 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
LAP3P2	ENST00000454686.1	n.1406C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33145 AN: 152002 Hom.: 4446 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.219

GnomAD4 exome AF: 0.148 AC: 201075 AN: 1362794 Hom.: 19802 Cov.: 25 AF XY: 0.146 AC XY: 99320 AN XY: 681476

Gnomad4 AFR exome AF: 0.317

Gnomad4 AMR exome AF: 0.412

Gnomad4 ASJ exome AF: 0.0909

Gnomad4 EAS exome AF: 0.467

Gnomad4 SAS exome AF: 0.109

Gnomad4 FIN exome AF: 0.111

Gnomad4 NFE exome AF: 0.126

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.218 AC: 33204 AN: 152120 Hom.: 4461 Cov.: 32 AF XY: 0.219 AC XY: 16275 AN XY: 74350

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.0957

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.218

Alfa AF: 0.0470 Hom.: 61

Bravo AF: 0.246

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	13
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12192877; hg19: chr6-36642999; COSMIC: COSV55191963;