rs4714003

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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 -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_109836.1. 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.644G>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAP3P2	ENST00000454686.1	TSL:6	n.667C>A		non_coding_transcript_exon	Exon 1 of 1
	PANDAR	ENST00000629595.1	TSL:6	n.644G>T		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.000162 AC: 5 AN: 30786

American (AMR) AF: 0.00306 AC: 136 AN: 44448

Ashkenazi Jewish (ASJ) AF: 0.00109 AC: 28 AN: 25678

East Asian (EAS) AF: 0.00 AC: 0 AN: 38966

South Asian (SAS) AF: 0.000460 AC: 39 AN: 84700

European-Finnish (FIN) AF: 0.000244 AC: 13 AN: 53352

Middle Eastern (MID) AF: 0.000714 AC: 4 AN: 5606

European-Non Finnish (NFE) AF: 0.00178 AC: 1842 AN: 1034614

Other (OTH) AF: 0.00160 AC: 92 AN: 57394

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

African (AFR) AF: 0.000338 AC: 14 AN: 41454

American (AMR) AF: 0.00360 AC: 55 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.000622 AC: 3 AN: 4826

European-Finnish (FIN) AF: 0.000472 AC: 5 AN: 10598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00194 AC: 132 AN: 67994

Other (OTH) AF: 0.00 AC: 0 AN: 2108

Alfa AF: 0.00 Hom.: 117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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