rs10947622

Variant names:

• chr6-36674625-C-T
• rs10947622
• ENST00000454686.1:n.809C>T

Variant summary

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

The ENST00000454686.1(LAP3P2):​n.809C>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 0.191 in 1,129,798 control chromosomes in the GnomAD database, including 25,803 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 (4478 hom., cov: 32)
  • Exomes 𝑓: 0.19 (21325 hom.)
• Consequence: LAP3P2 ENST00000454686.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 5 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=-0.59).
• 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.502G>A		non_coding_transcript_exon_variant	Exon 1 of 1
LAP3P2		n.36674625C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAP3P2	ENST00000454686.1	n.809C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
PANDAR	ENST00000629595.1	n.502G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33179 AN: 152002 Hom.: 4463 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.219

GnomAD4 exome AF: 0.187 AC: 182378 AN: 977678 Hom.: 21325 Cov.: 15 AF XY: 0.180 AC XY: 91031 AN XY: 506636

African (AFR) AF: 0.359 AC: 9019 AN: 25134

American (AMR) AF: 0.421 AC: 18520 AN: 44016

Ashkenazi Jewish (ASJ) AF: 0.0988 AC: 2279 AN: 23058

East Asian (EAS) AF: 0.477 AC: 18050 AN: 37868

South Asian (SAS) AF: 0.118 AC: 8987 AN: 76276

European-Finnish (FIN) AF: 0.113 AC: 5981 AN: 53138

Middle Eastern (MID) AF: 0.182 AC: 887 AN: 4870

European-Non Finnish (NFE) AF: 0.165 AC: 110496 AN: 668870

Other (OTH) AF: 0.184 AC: 8159 AN: 44448

GnomAD4 genome AF: 0.218 AC: 33238 AN: 152120 Hom.: 4478 Cov.: 32 AF XY: 0.219 AC XY: 16298 AN XY: 74354

African (AFR) AF: 0.330 AC: 13680 AN: 41478

American (AMR) AF: 0.323 AC: 4931 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 332 AN: 3472

East Asian (EAS) AF: 0.422 AC: 2177 AN: 5160

South Asian (SAS) AF: 0.122 AC: 589 AN: 4822

European-Finnish (FIN) AF: 0.119 AC: 1255 AN: 10578

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

European-Non Finnish (NFE) AF: 0.142 AC: 9637 AN: 68002

Other (OTH) AF: 0.218 AC: 461 AN: 2114

Alfa AF: 0.185 Hom.: 435

Bravo AF: 0.246

Asia WGS AF: 0.251 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	9.1
DANN	Benign	0.73
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs10947622; hg19: chr6-36642402; COSMIC: COSV55190013;