rs1977172

Variant names:

• chr6-36673977-A-C
• rs1977172
• ENST00000454686.1:n.161A>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000454686.1(LAP3P2):​n.161A>C 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: LAP3P2 ENST00000454686.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 15 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454686.1. 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.1150T>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAP3P2	ENST00000454686.1	TSL:6	n.161A>C		non_coding_transcript_exon	Exon 1 of 1
	PANDAR	ENST00000629595.1	TSL:6	n.1150T>G		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.939 AC: 31146 AN: 33174

American (AMR) AF: 0.912 AC: 40785 AN: 44700

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 20935 AN: 26086

East Asian (EAS) AF: 0.870 AC: 34466 AN: 39602

South Asian (SAS) AF: 0.926 AC: 79803 AN: 86140

European-Finnish (FIN) AF: 0.846 AC: 45206 AN: 53416

Middle Eastern (MID) AF: 0.837 AC: 4806 AN: 5742

European-Non Finnish (NFE) AF: 0.878 AC: 969926 AN: 1104926

Other (OTH) AF: 0.886 AC: 53210 AN: 60084

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

African (AFR) AF: 0.938 AC: 39004 AN: 41576

American (AMR) AF: 0.897 AC: 13731 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2759 AN: 3470

East Asian (EAS) AF: 0.893 AC: 4625 AN: 5182

South Asian (SAS) AF: 0.933 AC: 4498 AN: 4820

European-Finnish (FIN) AF: 0.840 AC: 8881 AN: 10576

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59433 AN: 68012

Other (OTH) AF: 0.883 AC: 1867 AN: 2114

Alfa AF: 0.882 Hom.: 17102

Bravo AF: 0.898

Asia WGS AF: 0.929 AC: 3232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.74
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs1977172; hg19: chr6-36641754;