rs689462

Variant names:

• chr1-186681951-T-G
• rs689462
• ENST00000608917.4:n.1844T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000608917.4(PACERR):​n.1844T>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 ENST00000608917.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PACERR	ENST00000608917.4	n.1844T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.270 AC: 11159 AN: 41354

American (AMR) AF: 0.0464 AC: 707 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3470

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5176

South Asian (SAS) AF: 0.0614 AC: 295 AN: 4802

European-Finnish (FIN) AF: 0.0153 AC: 162 AN: 10558

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0237 AC: 1610 AN: 67926

Other (OTH) AF: 0.0720 AC: 152 AN: 2112

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs689462; hg19: chr1-186651083;