Genetic Variant PGR-AS1:n.1209-16869T>C (chr11-101178616-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000632820.1(PGR-AS1):n.1209-16869T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,038 control chromosomes in the GnomAD database, including 6,398 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 0.25 ( 6398 hom., cov: 32)

Consequence

PGR-AS1
ENST00000632820.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.42

Publications

14 publications found

Variant links:

Genes affected

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

PGR-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PGR-AS1	ENST00000632820.1 link	n.1209-16869T>C	intron_variant	Intron 5 of 6	1
PGR-AS1	ENST00000531772.2 link	n.523+19361T>C	intron_variant	Intron 5 of 5	2
PGR-AS1	ENST00000843145.1 link	n.573+19361T>C	intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38304

AN:

151920

Hom.:

6397

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.888

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.233

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

GnomAD4 genome

AF:

0.252

AC:

38329

AN:

152038

Hom.:

6398

Cov.:

AF XY:

0.258

AC XY:

19194

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.302

AC:

12511

AN:

41448

American (AMR)

AF:

0.276

AC:

4218

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

593

AN:

3466

East Asian (EAS)

AF:

0.888

AC:

4589

AN:

5168

South Asian (SAS)

AF:

0.413

AC:

1988

AN:

4808

European-Finnish (FIN)

AF:

0.181

AC:

1917

AN:

10592

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.175

AC:

11881

AN:

67974

Other (OTH)

AF:

0.235

AC:

497

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1299

2597

3896

5194

6493

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.207

Hom.:

12421

Bravo

AF:

0.264

Asia WGS

AF:

0.591

AC:

2052

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.4

(source)

DANN

Benign

0.71

PhyloP100

1.4

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over