1-186681619-T-C

Variant names:

• chr1-186681619-T-C
• rs689466
• ENST00000608917.4:n.1512T>C

Variant summary

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

The ENST00000608917.4(PACERR):​n.1512T>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 0.175 in 152,090 control chromosomes in the GnomAD database, including 2,773 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 0.18 (2773 hom., cov: 32)
• Consequence: PACERR ENST00000608917.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 287 publications found

Genes affected

PACERR (HGNC:50552): (PTGS2 antisense NFKB1 complex-mediated expression regulator RNA) This gene represents transcription of a long non-coding RNA produced in antisense to the prostaglandin-endoperoxide synthase 2 (PTGS2) gene. This transcript interacts with NF-kB transcriptional regulators to promote expression of PTGS2. [provided by RefSeq, Feb 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PACERR	NR_125801.1	n.*173T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PACERR	ENST00000608917.4	n.1512T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26654 AN: 151972 Hom.: 2776 Cov.: 32

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.188

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.175 AC: 26658 AN: 152090 Hom.: 2773 Cov.: 32 AF XY: 0.182 AC XY: 13494 AN XY: 74330

African (AFR) AF: 0.0941 AC: 3907 AN: 41514

American (AMR) AF: 0.258 AC: 3942 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3466

East Asian (EAS) AF: 0.465 AC: 2394 AN: 5152

South Asian (SAS) AF: 0.147 AC: 710 AN: 4826

European-Finnish (FIN) AF: 0.214 AC: 2262 AN: 10568

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12294 AN: 67970

Other (OTH) AF: 0.188 AC: 397 AN: 2108

Alfa AF: 0.183 Hom.: 5968

Bravo AF: 0.181

Asia WGS AF: 0.286 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.53
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs689466; hg19: chr1-186650751;