1-186682744-G-T

Position:

• chr1-186682744-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000608917.3(PACERR):​n.2144G>T 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 0.201 in 152,044 control chromosomes in the GnomAD database, including 3,772 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 0.20 (3772 hom., cov: 32)
• Consequence: PACERR ENST00000608917.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PACERR	ENST00000608917.3	n.2144G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30496 AN: 151926 Hom.: 3773 Cov.: 32

Gnomad AFR AF: 0.0602

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.201 AC: 30489 AN: 152044 Hom.: 3772 Cov.: 32 AF XY: 0.201 AC XY: 14944 AN XY: 74320

Gnomad4 AFR AF: 0.0600

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.195

Alfa AF: 0.179 Hom.: 765

Bravo AF: 0.185

Asia WGS AF: 0.216 AC: 752 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12042763; hg19: chr1-186651876;