rs10501973

Positions:

• chr11-101192845-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000632820.1(PGR-AS1):​n.1209-2640G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.901

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGR-AS1	ENST00000632820.1	n.1209-2640G>A		intron_variant, non_coding_transcript_variant		1
PGR-AS1	ENST00000531772.1	n.181-16498G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30061 AN: 151742 Hom.: 3732 Cov.: 32

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.: 32 AF XY: 0.197 AC XY: 14622 AN XY: 74202

Gnomad4 AFR AF: 0.0583

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.00522

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.195

Alfa AF: 0.243 Hom.: 622

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
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501973; hg19: chr11-101063576;