chr11-101192200-G-A

Variant names:

• chr11-101192200-G-A
• rs954723
• ENST00000632820.1:n.1209-3285G>A

Variant summary

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

The ENST00000632820.1(PGR-AS1):​n.1209-3285G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,850 control chromosomes in the GnomAD database, including 16,551 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 0.45 (16551 hom., cov: 32)
• Consequence: PGR-AS1 ENST00000632820.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 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.1209-3285G>A		intron_variant	Intron 5 of 6	1
PGR-AS1	ENST00000531772.2	n.524-17143G>A		intron_variant	Intron 5 of 5	2
PGR-AS1	ENST00000843145.1	n.573+32945G>A		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67867 AN: 151732 Hom.: 16544 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.00753

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.447 AC: 67891 AN: 151850 Hom.: 16551 Cov.: 32 AF XY: 0.441 AC XY: 32759 AN XY: 74210

African (AFR) AF: 0.313 AC: 12950 AN: 41396

American (AMR) AF: 0.432 AC: 6585 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1385 AN: 3464

East Asian (EAS) AF: 0.00754 AC: 39 AN: 5170

South Asian (SAS) AF: 0.397 AC: 1910 AN: 4814

European-Finnish (FIN) AF: 0.504 AC: 5306 AN: 10526

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.562 AC: 38189 AN: 67930

Other (OTH) AF: 0.448 AC: 945 AN: 2110

Alfa AF: 0.528 Hom.: 10724

Bravo AF: 0.435

Asia WGS AF: 0.185 AC: 645 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.82
DANN	Benign	0.47
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs954723; hg19: chr11-101062931;