11-101137771-T-C

Variant names:

• chr11-101137771-T-C
• rs4754732
• ENST00000632820.1:n.1021+4646T>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.1021+4646T>C variant causes a intron 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 ENST00000632820.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 9 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=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000632820.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGR-AS1	NR_073144.1		n.1021+4646T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGR-AS1	ENST00000632820.1	TSL:1	n.1021+4646T>C		intron	N/A
	PGR-AS1	ENST00000531772.2	TSL:2	n.336+4641T>C		intron	N/A
	PGR-AS1	ENST00000843145.1		n.386+4646T>C		intron	N/A

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

African (AFR) AF: 0.0933 AC: 3877 AN: 41558

American (AMR) AF: 0.232 AC: 3554 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3468

East Asian (EAS) AF: 0.00579 AC: 30 AN: 5184

South Asian (SAS) AF: 0.206 AC: 996 AN: 4830

European-Finnish (FIN) AF: 0.310 AC: 3282 AN: 10578

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.316 AC: 21474 AN: 67972

Other (OTH) AF: 0.222 AC: 468 AN: 2110

Alfa AF: 0.265 Hom.: 976

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.3
DANN	Benign	0.83
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs4754732; hg19: chr11-101008502;