rs10947623

Variant names:

• chr6-36675059-G-A
• rs10947623
• ENST00000454686.1:n.1243G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-36675059-G-A
• chr6-36675059-G-T

Variant summary

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

The ENST00000454686.1(LAP3P2):​n.1243G>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 0.16 in 1,433,524 control chromosomes in the GnomAD database, including 24,385 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 (4464 hom., cov: 33)
  • Exomes 𝑓: 0.15 (19921 hom.)
• Consequence: LAP3P2 ENST00000454686.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• Publications: 11 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=-0.67).
• 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
PANDAR	NR_109836.1	n.68C>T		non_coding_transcript_exon_variant	Exon 1 of 1
LAP3P2		n.36675059G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAP3P2	ENST00000454686.1	n.1243G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
PANDAR	ENST00000629595.1	n.68C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33141 AN: 152044 Hom.: 4449 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.422

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: 0.153 AC: 195606 AN: 1281362 Hom.: 19921 Cov.: 24 AF XY: 0.150 AC XY: 97071 AN XY: 646386

African (AFR) AF: 0.324 AC: 9497 AN: 29284

American (AMR) AF: 0.419 AC: 18531 AN: 44196

Ashkenazi Jewish (ASJ) AF: 0.0935 AC: 2338 AN: 25000

East Asian (EAS) AF: 0.469 AC: 18060 AN: 38490

South Asian (SAS) AF: 0.111 AC: 9181 AN: 82636

European-Finnish (FIN) AF: 0.112 AC: 5915 AN: 52736

Middle Eastern (MID) AF: 0.175 AC: 942 AN: 5396

European-Non Finnish (NFE) AF: 0.129 AC: 122562 AN: 949696

Other (OTH) AF: 0.159 AC: 8580 AN: 53928

GnomAD4 genome AF: 0.218 AC: 33200 AN: 152162 Hom.: 4464 Cov.: 33 AF XY: 0.219 AC XY: 16291 AN XY: 74402

African (AFR) AF: 0.329 AC: 13655 AN: 41464

American (AMR) AF: 0.322 AC: 4925 AN: 15280

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

East Asian (EAS) AF: 0.421 AC: 2182 AN: 5182

South Asian (SAS) AF: 0.122 AC: 591 AN: 4830

European-Finnish (FIN) AF: 0.118 AC: 1249 AN: 10606

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

European-Non Finnish (NFE) AF: 0.142 AC: 9632 AN: 68016

Other (OTH) AF: 0.218 AC: 460 AN: 2112

Alfa AF: 0.174 Hom.: 10706

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	-0.67
CADD	Benign	6.3
DANN	Benign	0.77
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs10947623; hg19: chr6-36642836; COSMIC: COSV55188689;