chr11-101173472-T-C

Variant names:

• chr11-101173472-T-C
• rs471811
• ENST00000632820.1:n.1208+14217T>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.1208+14217T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,916 control chromosomes in the GnomAD database, including 34,602 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 0.67 (34602 hom., cov: 31)
• Consequence: PGR-AS1 ENST00000632820.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 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.1208+14217T>C		intron_variant	Intron 5 of 6	1
PGR-AS1	ENST00000531772.2	n.523+14217T>C		intron_variant	Intron 5 of 5	2
PGR-AS1	ENST00000843145.1	n.573+14217T>C		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101560 AN: 151798 Hom.: 34563 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.669 AC: 101646 AN: 151916 Hom.: 34602 Cov.: 31 AF XY: 0.675 AC XY: 50139 AN XY: 74252

African (AFR) AF: 0.562 AC: 23273 AN: 41430

American (AMR) AF: 0.747 AC: 11390 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2462 AN: 3466

East Asian (EAS) AF: 0.987 AC: 5098 AN: 5164

South Asian (SAS) AF: 0.755 AC: 3635 AN: 4814

European-Finnish (FIN) AF: 0.706 AC: 7440 AN: 10540

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46108 AN: 67934

Other (OTH) AF: 0.684 AC: 1443 AN: 2110

Alfa AF: 0.677 Hom.: 4352

Bravo AF: 0.668

Asia WGS AF: 0.866 AC: 3001 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.50
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs471811; hg19: chr11-101044203;