rs689462

Positions:

• chr1-186681951-T-G

Variant summary

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

The ENST00000608917.3(PACERR):​n.1351T>G 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 0.0938 in 151,850 control chromosomes in the GnomAD database, including 1,594 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 0.094 (1594 hom., cov: 31)
• Consequence: PACERR ENST00000608917.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 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.1351T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0937 AC: 14210 AN: 151732 Hom.: 1586 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0464

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0616

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0237

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0938 AC: 14246 AN: 151850 Hom.: 1594 Cov.: 31 AF XY: 0.0918 AC XY: 6814 AN XY: 74216

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.0464

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0614

Gnomad4 FIN AF: 0.0153

Gnomad4 NFE AF: 0.0237

Gnomad4 OTH AF: 0.0720

Alfa AF: 0.0863 Hom.: 259

Bravo AF: 0.103

Asia WGS AF: 0.0480 AC: 167 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs689462; hg19: chr1-186651083;