rs12192877

Variant names:

• chr6-36675222-C-A
• rs12192877
• ENST00000454686.1:n.1406C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-36675222-C-A
• chr6-36675222-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

PANDAR (HGNC:44048): (promoter of CDKN1A antisense DNA damage activated RNA) This gene produces a non-coding RNA that is thought to regulate the response to DNA damage. This gene is induced by tumor protein p53 and interacts with and modulates the activity of a transcription factor that induce pro-apoptotic genes. Deregulation of this gene is associated with cancer progression. [provided by RefSeq, Dec 2017]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LAP3P2		n.36675222C>A		intragenic_variant
PANDAR	NR_109836.1	n.-96G>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAP3P2	ENST00000454686.1	n.1406C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
PANDAR	ENST00000629595.1	n.-96G>T		upstream_gene_variant		6

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

African (AFR) AF: 0.317 AC: 9536 AN: 30124

American (AMR) AF: 0.412 AC: 17217 AN: 41828

Ashkenazi Jewish (ASJ) AF: 0.0909 AC: 2206 AN: 24272

East Asian (EAS) AF: 0.467 AC: 17977 AN: 38514

South Asian (SAS) AF: 0.109 AC: 8919 AN: 81928

European-Finnish (FIN) AF: 0.111 AC: 5753 AN: 51654

Middle Eastern (MID) AF: 0.166 AC: 806 AN: 4848

European-Non Finnish (NFE) AF: 0.126 AC: 129950 AN: 1033146

Other (OTH) AF: 0.154 AC: 8711 AN: 56480

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

African (AFR) AF: 0.330 AC: 13664 AN: 41466

American (AMR) AF: 0.323 AC: 4933 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2172 AN: 5160

South Asian (SAS) AF: 0.122 AC: 588 AN: 4824

European-Finnish (FIN) AF: 0.118 AC: 1248 AN: 10590

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9630 AN: 68000

Other (OTH) AF: 0.218 AC: 461 AN: 2116

Alfa AF: 0.106 Hom.: 235

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
PhyloP100		2.9

Splicing

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

Other links and lift over

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