ENST00000608917.3:n.1153_1154delAC

Variant names:

• chr1-186681744-TAC-T
• rs689464
• ENST00000608917.3:n.1153_1154delAC

Variant summary

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

The ENST00000608917.3(PACERR):​n.1153_1154delAC 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PACERR	ENST00000608917.3	n.1153_1154delAC		non_coding_transcript_exon_variant	Exon 1 of 1	6

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;