chr6-36673769-C-A

Variant names:

• chr6-36673769-C-A
• rs12199346
• ENST00000629595.1:n.1358G>T

Variant summary

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

The ENST00000629595.1(PANDAR):​n.1358G>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 0.232 in 1,050,742 control chromosomes in the GnomAD database, including 29,540 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 (3614 hom., cov: 32)
  • Exomes 𝑓: 0.23 (25926 hom.)
• Consequence: PANDAR ENST00000629595.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 13 publications found

Genes affected

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]

LAP3P2 (HGNC:42365): (leucine aminopeptidase 3 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000629595.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PANDAR	NR_109836.1		n.1358G>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PANDAR	ENST00000629595.1	TSL:6	n.1358G>T		non_coding_transcript_exon	Exon 1 of 1
	LAP3P2	ENST00000454686.1	TSL:6	n.-48C>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32743 AN: 151974 Hom.: 3606 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.248

GnomAD4 exome AF: 0.235 AC: 211165 AN: 898650 Hom.: 25926 Cov.: 12 AF XY: 0.240 AC XY: 113006 AN XY: 470494

African (AFR) AF: 0.176 AC: 3911 AN: 22214

American (AMR) AF: 0.149 AC: 6397 AN: 42940

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 7004 AN: 22306

East Asian (EAS) AF: 0.143 AC: 5317 AN: 37070

South Asian (SAS) AF: 0.314 AC: 23256 AN: 74064

European-Finnish (FIN) AF: 0.190 AC: 9957 AN: 52428

Middle Eastern (MID) AF: 0.280 AC: 1179 AN: 4204

European-Non Finnish (NFE) AF: 0.239 AC: 143788 AN: 601928

Other (OTH) AF: 0.250 AC: 10356 AN: 41496

GnomAD4 genome AF: 0.215 AC: 32757 AN: 152092 Hom.: 3614 Cov.: 32 AF XY: 0.213 AC XY: 15802 AN XY: 74356

African (AFR) AF: 0.171 AC: 7081 AN: 41492

American (AMR) AF: 0.199 AC: 3037 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3470

East Asian (EAS) AF: 0.169 AC: 876 AN: 5174

South Asian (SAS) AF: 0.316 AC: 1520 AN: 4810

European-Finnish (FIN) AF: 0.192 AC: 2031 AN: 10580

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.240 AC: 16336 AN: 67986

Other (OTH) AF: 0.255 AC: 537 AN: 2110

Alfa AF: 0.213 Hom.: 2586

Bravo AF: 0.209

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.82
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs12199346; hg19: chr6-36641546; COSMIC: COSV55188849;