1-186681714-T-C

Variant names:

• chr1-186681714-T-C
• rs689465
• ENST00000608917.3:n.1114T>C

Variant summary

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

The ENST00000608917.3(PACERR):​n.1114T>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 0.137 in 150,656 control chromosomes in the GnomAD database, including 1,487 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 0.14 (1487 hom., cov: 31)
• Consequence: PACERR ENST00000608917.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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.1114T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20550 AN: 150546 Hom.: 1478 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0465

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.137 AC: 20578 AN: 150656 Hom.: 1487 Cov.: 31 AF XY: 0.133 AC XY: 9811 AN XY: 73656

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.0463

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.160

Alfa AF: 0.148 Hom.: 1606

Bravo AF: 0.143

Asia WGS AF: 0.131 AC: 457 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.95
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs689465; hg19: chr1-186650846;