rs1893505

chr11-101196977-T-C

Variant summary

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

The ENST00000632820.1(PGR-AS1):n.1363+1338T>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 0.515 in 151,850 control chromosomes in the GnomAD database, including 21,525 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 0.52 (21525 hom., cov: 32)
• Consequence: PGR-AS1 ENST00000632820.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGR-AS1	ENST00000632820.1	n.1363+1338T>C		intron_variant, non_coding_transcript_variant		1
PGR-AS1	ENST00000531772.1	n.181-12366T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78215 AN: 151730 Hom.: 21504 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.515 AC: 78271 AN: 151850 Hom.: 21525 Cov.: 32 AF XY: 0.513 AC XY: 38051 AN XY: 74232

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.0780

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.538

Alfa AF: 0.565 Hom.: 7709

Bravo AF: 0.502

Asia WGS AF: 0.268 AC: 935 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.1
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893505; hg19: chr11-101067708;