6-36675194-C-T

Variant names:

• chr6-36675194-C-T
• rs12192827
• ENST00000454686.1:n.1378C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000454686.1(LAP3P2):​n.1378C>T 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 1,437,586 control chromosomes in the GnomAD database, including 23,342 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 (4468 hom., cov: 32)
  • Exomes 𝑓: 0.15 (18874 hom.)
• Consequence: LAP3P2 ENST00000454686.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16
• Publications: 3 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=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454686.1. 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
	PANDAR	NR_109836.1		n.-68G>A		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAP3P2	ENST00000454686.1	TSL:6	n.1378C>T		non_coding_transcript_exon	Exon 1 of 1
	PANDAR	ENST00000629595.1	TSL:6	n.-68G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33166 AN: 152046 Hom.: 4453 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.218

GnomAD4 exome AF: 0.147 AC: 189074 AN: 1285422 Hom.: 18874 Cov.: 21 AF XY: 0.145 AC XY: 94097 AN XY: 648090

African (AFR) AF: 0.316 AC: 9080 AN: 28732

American (AMR) AF: 0.416 AC: 18108 AN: 43528

Ashkenazi Jewish (ASJ) AF: 0.0912 AC: 2257 AN: 24736

East Asian (EAS) AF: 0.467 AC: 17844 AN: 38190

South Asian (SAS) AF: 0.109 AC: 9001 AN: 82462

European-Finnish (FIN) AF: 0.112 AC: 5841 AN: 52250

Middle Eastern (MID) AF: 0.168 AC: 884 AN: 5272

European-Non Finnish (NFE) AF: 0.123 AC: 117728 AN: 956138

Other (OTH) AF: 0.154 AC: 8331 AN: 54114

GnomAD4 genome AF: 0.218 AC: 33225 AN: 152164 Hom.: 4468 Cov.: 32 AF XY: 0.219 AC XY: 16285 AN XY: 74376

African (AFR) AF: 0.330 AC: 13679 AN: 41498

American (AMR) AF: 0.322 AC: 4930 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 331 AN: 3462

East Asian (EAS) AF: 0.422 AC: 2182 AN: 5176

South Asian (SAS) AF: 0.121 AC: 586 AN: 4826

European-Finnish (FIN) AF: 0.118 AC: 1251 AN: 10588

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

European-Non Finnish (NFE) AF: 0.142 AC: 9631 AN: 68006

Other (OTH) AF: 0.217 AC: 459 AN: 2112

Alfa AF: 0.172 Hom.: 582

Bravo AF: 0.246

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.63
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs12192827; hg19: chr6-36642971; COSMIC: COSV55190844;