Genetic Variant ENST00000632820.1: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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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