Genetic Variant PGR-AS1:n.1021+4646T>C (chr11-101137771-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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.324

Publications

9 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=-0.7).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PGR-AS1	NR_073144.1 link	n.1021+4646T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PGR-AS1	ENST00000632820.1 link	n.1021+4646T>C	intron_variant	Intron 3 of 6	1
PGR-AS1	ENST00000531772.2 link	n.336+4641T>C	intron_variant	Intron 3 of 5	2
PGR-AS1	ENST00000843145.1 link	n.386+4646T>C	intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.228

AC:

34725

AN:

152086

Hom.:

4717

Cov.:

show subpopulations

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.:

AF XY:

0.229

AC XY:

17014

AN XY:

74412

show subpopulations

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:

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:

AN:

292

European-Non Finnish (NFE)

AF:

0.316

AC:

21474

AN:

67972

Other (OTH)

AF:

0.222

AC:

468

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1328

2657

3985

5314

6642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

362

724

1086

1448

1810

<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:

0.265

Hom.:

976

Bravo

AF:

0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

5.3

(source)

DANN

Benign

0.83

PhyloP100

0.32

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