rs4714003

Positions:

• chr6-36674483-C-A
• chr6-36674483-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_109836.1(PANDAR):​n.644G>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 0.00156 in 1,527,664 control chromosomes in the GnomAD database, including 6 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 0.0015 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0016 (3 hom.)
• Consequence: PANDAR NR_109836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BS2: High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PANDAR	NR_109836.1	n.644G>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LAP3P2	ENST00000454686.1	n.667C>A		non_coding_transcript_exon_variant	1/1
PANDAR	ENST00000629595.1	n.644G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.00151 AC: 230 AN: 152002 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.000339

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.00360

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.000472

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00194

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00157 AC: 2159 AN: 1375544 Hom.: 3 Cov.: 26 AF XY: 0.00157 AC XY: 1079 AN XY: 688868

Gnomad4 AFR exome AF: 0.000162

Gnomad4 AMR exome AF: 0.00306

Gnomad4 ASJ exome AF: 0.00109

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000460

Gnomad4 FIN exome AF: 0.000244

Gnomad4 NFE exome AF: 0.00178

Gnomad4 OTH exome AF: 0.00160

GnomAD4 genome AF: 0.00151 AC: 230 AN: 152120 Hom.: 3 Cov.: 32 AF XY: 0.00149 AC XY: 111 AN XY: 74384

Gnomad4 AFR AF: 0.000338

Gnomad4 AMR AF: 0.00360

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.000472

Gnomad4 NFE AF: 0.00194

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.0030
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4714003; hg19: chr6-36642260;