11-101137771-T-C

Variant summary

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

The NR_073144.1(PGR-AS1):n.1021+4646T>C 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 0.228 in 152,204 control chromosomes in the GnomAD database, including 4,717 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 0.23 (4717 hom., cov: 32)
• Consequence: PGR-AS1 NR_073144.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324

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=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGR-AS1	NR_073144.1	n.1021+4646T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGR-AS1	ENST00000632820.1	n.1021+4646T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34725 AN: 152086 Hom.: 4717 Cov.: 32

Gnomad AFR AF: 0.0932

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.228 AC: 34737 AN: 152204 Hom.: 4717 Cov.: 32 AF XY: 0.229 AC XY: 17014 AN XY: 74412

Gnomad4 AFR AF: 0.0933

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.00579

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.222

Alfa AF: 0.265 Hom.: 976

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	5.3
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4754732; hg19: chr11-101008502;