1-186681744-TAC-T

Variant names:

• chr1-186681744-TAC-T
• rs689464
• ENST00000608917.4:n.1646_1647delAC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000608917.4(PACERR):​n.1646_1647delAC 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 0.0824 in 151,732 control chromosomes in the GnomAD database, including 1,202 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.082 (1202 hom., cov: 30)
• Consequence: PACERR ENST00000608917.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 2 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000608917.4. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PACERR	ENST00000608917.4	TSL:6	n.1646_1647delAC		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12465 AN: 151616 Hom.: 1194 Cov.: 30

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0149

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0238

Gnomad OTH AF: 0.0642

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

GnomAD4 genome AF: 0.0824 AC: 12499 AN: 151732 Hom.: 1202 Cov.: 30 AF XY: 0.0804 AC XY: 5965 AN XY: 74196

African (AFR) AF: 0.235 AC: 9681 AN: 41260

American (AMR) AF: 0.0411 AC: 626 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3464

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5176

South Asian (SAS) AF: 0.0259 AC: 125 AN: 4818

European-Finnish (FIN) AF: 0.0149 AC: 157 AN: 10508

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0238 AC: 1615 AN: 67944

Other (OTH) AF: 0.0640 AC: 135 AN: 2110

Alfa AF: 0.00485 Hom.: 2

Asia WGS AF: 0.0280 AC: 97 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs689464; hg19: chr1-186650876;