1-186682744-G-T

Variant names:

• chr1-186682744-G-T
• rs12042763
• ENST00000608917.4:n.2637G>T

Variant summary

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

The ENST00000608917.4(PACERR):​n.2637G>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 ENST00000608917.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423
• Publications: 21 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000608917.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PACERR	ENST00000608917.4	TSL:6	n.2637G>T		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.0600 AC: 2489 AN: 41500

American (AMR) AF: 0.198 AC: 3029 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3466

East Asian (EAS) AF: 0.263 AC: 1359 AN: 5160

South Asian (SAS) AF: 0.243 AC: 1169 AN: 4820

European-Finnish (FIN) AF: 0.298 AC: 3143 AN: 10546

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17748 AN: 67948

Other (OTH) AF: 0.195 AC: 411 AN: 2108

Alfa AF: 0.199 Hom.: 1506

Bravo AF: 0.185

Asia WGS AF: 0.216 AC: 752 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.45
PhyloP100		0.42

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12042763;

hg19: chr1-186651876;