ENST00000632820.1:n.1363+1338T>C

Variant names:

• chr11-101196977-T-C
• rs1893505
• ENST00000632820.1:n.1363+1338T>C

Variant summary

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

The ENST00000632820.1(PGR-AS1):​n.1363+1338T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PGR-AS1	ENST00000632820.1	n.1363+1338T>C		intron_variant	Intron 6 of 6	1
PGR-AS1	ENST00000531772.2	n.524-12366T>C		intron_variant	Intron 5 of 5	2
PGR-AS1	ENST00000843145.1	n.573+37722T>C		intron_variant	Intron 5 of 6

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

African (AFR) AF: 0.377 AC: 15643 AN: 41452

American (AMR) AF: 0.530 AC: 8086 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1804 AN: 3466

East Asian (EAS) AF: 0.0780 AC: 404 AN: 5178

South Asian (SAS) AF: 0.466 AC: 2245 AN: 4814

European-Finnish (FIN) AF: 0.604 AC: 6387 AN: 10572

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41896 AN: 67788

Other (OTH) AF: 0.538 AC: 1134 AN: 2108

Alfa AF: 0.565 Hom.: 9745

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1893505; hg19: chr11-101067708;