rs568157

chr11-101153551-A-G

Variant summary

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

The NR_073144.1(PGR-AS1):n.1111+5319A>G 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 0.394 in 152,008 control chromosomes in the GnomAD database, including 12,730 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 0.39 (12730 hom., cov: 32)
• Consequence: PGR-AS1 NR_073144.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGR-AS1	NR_073144.1	n.1111+5319A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGR-AS1	ENST00000632820.1	n.1111+5319A>G		intron_variant, non_coding_transcript_variant		1
PGR-AS1	ENST00000531772.1	n.83+5319A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59835 AN: 151888 Hom.: 12718 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.0190

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.394 AC: 59885 AN: 152008 Hom.: 12730 Cov.: 32 AF XY: 0.392 AC XY: 29107 AN XY: 74284

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.0190

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.392

Alfa AF: 0.455 Hom.: 32083

Bravo AF: 0.381

Asia WGS AF: 0.174 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.36
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs568157; hg19: chr11-101024282;