6-36674483-C-T

Variant names:

• chr6-36674483-C-T
• rs4714003
• ENST00000454686.1:n.667C>T

Variant summary

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

The ENST00000454686.1(LAP3P2):​n.667C>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 0.156 in 1,519,996 control chromosomes in the GnomAD database, including 25,145 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 (4690 hom., cov: 32)
  • Exomes 𝑓: 0.15 (20455 hom.)
• Consequence: LAP3P2 ENST00000454686.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 4 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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PANDAR	NR_109836.1	n.644G>A		non_coding_transcript_exon_variant	Exon 1 of 1
LAP3P2		n.36674483C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAP3P2	ENST00000454686.1	n.667C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
PANDAR	ENST00000629595.1	n.644G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33773 AN: 151954 Hom.: 4670 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.148 AC: 202665 AN: 1367924 Hom.: 20455 Cov.: 26 AF XY: 0.146 AC XY: 100193 AN XY: 685374

African (AFR) AF: 0.331 AC: 10110 AN: 30508

American (AMR) AF: 0.419 AC: 18586 AN: 44362

Ashkenazi Jewish (ASJ) AF: 0.0926 AC: 2371 AN: 25608

East Asian (EAS) AF: 0.467 AC: 18175 AN: 38884

South Asian (SAS) AF: 0.110 AC: 9269 AN: 84494

European-Finnish (FIN) AF: 0.112 AC: 5968 AN: 53304

Middle Eastern (MID) AF: 0.170 AC: 947 AN: 5580

European-Non Finnish (NFE) AF: 0.125 AC: 128335 AN: 1028092

Other (OTH) AF: 0.156 AC: 8904 AN: 57092

GnomAD4 genome AF: 0.223 AC: 33846 AN: 152072 Hom.: 4690 Cov.: 32 AF XY: 0.223 AC XY: 16612 AN XY: 74352

African (AFR) AF: 0.344 AC: 14273 AN: 41436

American (AMR) AF: 0.324 AC: 4950 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3470

East Asian (EAS) AF: 0.422 AC: 2179 AN: 5164

South Asian (SAS) AF: 0.122 AC: 589 AN: 4824

European-Finnish (FIN) AF: 0.118 AC: 1254 AN: 10594

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

European-Non Finnish (NFE) AF: 0.142 AC: 9632 AN: 67982

Other (OTH) AF: 0.219 AC: 461 AN: 2108

Alfa AF: 0.0771 Hom.: 117

Bravo AF: 0.251

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.012
DANN	Benign	0.73
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs4714003; hg19: chr6-36642260; COSMIC: COSV55187275;