rs1977172

Positions:

• chr6-36673977-A-C
• chr6-36673977-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109836.1(PANDAR):​n.1150T>G 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 0.882 in 1,606,128 control chromosomes in the GnomAD database, including 625,115 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 0.89 (60805 hom., cov: 33)
  • Exomes 𝑓: 0.88 (564310 hom.)
• Consequence: PANDAR NR_109836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PANDAR	NR_109836.1	n.1150T>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LAP3P2	ENST00000454686.1	n.161A>C		non_coding_transcript_exon_variant	1/1
PANDAR	ENST00000629595.1	n.1150T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135788 AN: 152140 Hom.: 60750 Cov.: 33

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.882

GnomAD4 exome AF: 0.881 AC: 1280283 AN: 1453870 Hom.: 564310 Cov.: 34 AF XY: 0.882 AC XY: 638220 AN XY: 723878

Gnomad4 AFR exome AF: 0.939

Gnomad4 AMR exome AF: 0.912

Gnomad4 ASJ exome AF: 0.803

Gnomad4 EAS exome AF: 0.870

Gnomad4 SAS exome AF: 0.926

Gnomad4 FIN exome AF: 0.846

Gnomad4 NFE exome AF: 0.878

Gnomad4 OTH exome AF: 0.886

GnomAD4 genome AF: 0.893 AC: 135902 AN: 152258 Hom.: 60805 Cov.: 33 AF XY: 0.890 AC XY: 66208 AN XY: 74416

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.883

Alfa AF: 0.877 Hom.: 8622

Bravo AF: 0.898

Asia WGS AF: 0.929 AC: 3232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1977172; hg19: chr6-36641754;