dbSNP rs10501973: PGR-AS1:n.1209-2640G>A (chr11-101192845-G-A) – 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.1209-2640G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,860 control chromosomes in the GnomAD database, including 3,731 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 0.20 ( 3731 hom., cov: 32)

Consequence

PGR-AS1
ENST00000632820.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.901

Publications

2 publications found

Variant links:

Genes affected

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

PGR-AS1 links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 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.1209-2640G>A	intron_variant	Intron 5 of 6	1
PGR-AS1	ENST00000531772.2 link	n.524-16498G>A	intron_variant	Intron 5 of 5	2
PGR-AS1	ENST00000843145.1 link	n.573+33590G>A	intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

30061

AN:

151742

Hom.:

3732

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0584

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.215

Gnomad ASJ

AF:

0.152

Gnomad EAS

AF:

0.00521

Gnomad SAS

AF:

0.177

Gnomad FIN

AF:

0.255

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.198

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

GnomAD4 genome

AF:

0.198

AC:

30059

AN:

151860

Hom.:

3731

Cov.:

AF XY:

0.197

AC XY:

14622

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.0583

AC:

2416

AN:

41456

American (AMR)

AF:

0.215

AC:

3275

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.152

AC:

525

AN:

3460

East Asian (EAS)

AF:

0.00522

AC:

AN:

5168

South Asian (SAS)

AF:

0.178

AC:

858

AN:

4818

European-Finnish (FIN)

AF:

0.255

AC:

2686

AN:

10534

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.288

AC:

19553

AN:

67866

Other (OTH)

AF:

0.195

AC:

411

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1146

2291

3437

4582

5728

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.237

Hom.:

625

Bravo

AF:

0.188

Asia WGS

AF:

0.0880

AC:

306

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.8

(source)

DANN

Benign

0.41

PhyloP100

0.90

Splicing

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

Publications

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rs10501973

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