rs689464

Positions:

• chr1-186681744-TAC-T
• chr1-186681744-TAC-TACAC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000608917.3(PACERR):​n.1153_1154del 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 ENST00000608917.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

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

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PACERR	ENST00000608917.3	n.1153_1154del		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.0411

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0259

Gnomad4 FIN AF: 0.0149

Gnomad4 NFE AF: 0.0238

Gnomad4 OTH AF: 0.0640

Alfa AF: 0.00485 Hom.: 2

Asia WGS AF: 0.0280 AC: 97 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs689464; hg19: chr1-186650876;