rs507141

chr11-101132381-G-A

Variant summary

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

The NR_073144.1(PGR-AS1):n.907-630G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,120 control chromosomes in the GnomAD database, including 1,349 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 0.12 (1349 hom., cov: 33)
• Consequence: PGR-AS1 NR_073144.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

Genes affected

PGR-AS1 (HGNC:52650): (PGR antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGR-AS1	NR_073144.1	n.907-630G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGR-AS1	ENST00000632820.1	n.907-630G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17782 AN: 152002 Hom.: 1350 Cov.: 33

Gnomad AFR AF: 0.0303

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.117 AC: 17783 AN: 152120 Hom.: 1349 Cov.: 33 AF XY: 0.115 AC XY: 8544 AN XY: 74362

Gnomad4 AFR AF: 0.0302

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.0771

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.133

Alfa AF: 0.142 Hom.: 204

Bravo AF: 0.111

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs507141; hg19: chr11-101003112;