1-186683263-T-G

Variant names:

• chr1-186683263-T-G
• rs10911905
• ENST00000608917.4:n.*98T>G

Variant summary

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

The ENST00000608917.4(PACERR):​n.*98T>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,158 control chromosomes in the GnomAD database, including 1,474 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 (1474 hom., cov: 32)
• Consequence: PACERR ENST00000608917.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 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.*98T>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20567 AN: 152040 Hom.: 1465 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.135 AC: 20595 AN: 152158 Hom.: 1474 Cov.: 32 AF XY: 0.132 AC XY: 9819 AN XY: 74400

African (AFR) AF: 0.155 AC: 6441 AN: 41508

American (AMR) AF: 0.145 AC: 2217 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3470

East Asian (EAS) AF: 0.0470 AC: 243 AN: 5170

South Asian (SAS) AF: 0.138 AC: 666 AN: 4822

European-Finnish (FIN) AF: 0.0713 AC: 756 AN: 10600

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9133 AN: 67996

Other (OTH) AF: 0.159 AC: 335 AN: 2108

Alfa AF: 0.139 Hom.: 1245

Bravo AF: 0.143

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.43
PhyloP100		1.4

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: rs10911905;

hg19: chr1-186652395;