11-101143195-C-T

Variant names:

• chr11-101143195-C-T
• rs499590
• ENST00000632820.1:n.1022-4948C>T

Variant summary

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

The ENST00000632820.1(PGR-AS1):​n.1022-4948C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 150,760 control chromosomes in the GnomAD database, including 37,423 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 0.70 (37423 hom., cov: 28)
• Consequence: PGR-AS1 ENST00000632820.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PGR-AS1	NR_073144.1	n.1022-4948C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PGR-AS1	ENST00000632820.1	n.1022-4948C>T		intron_variant	Intron 3 of 6	1
PGR-AS1	ENST00000531772.2	n.337-4948C>T		intron_variant	Intron 3 of 5	2
PGR-AS1	ENST00000843145.1	n.387-4948C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.702 AC: 105742 AN: 150652 Hom.: 37377 Cov.: 28

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.626

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.702 AC: 105833 AN: 150760 Hom.: 37423 Cov.: 28 AF XY: 0.708 AC XY: 52109 AN XY: 73650

African (AFR) AF: 0.674 AC: 27767 AN: 41170

American (AMR) AF: 0.758 AC: 11515 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2487 AN: 3468

East Asian (EAS) AF: 0.987 AC: 5072 AN: 5140

South Asian (SAS) AF: 0.747 AC: 3568 AN: 4776

European-Finnish (FIN) AF: 0.710 AC: 7155 AN: 10080

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.680 AC: 45983 AN: 67642

Other (OTH) AF: 0.706 AC: 1482 AN: 2100

Alfa AF: 0.625 Hom.: 2540

Bravo AF: 0.704

Asia WGS AF: 0.874 AC: 3020 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.55
DANN	Benign	0.58
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs499590; hg19: chr11-101013926;