rs10501973

Variant names:

• chr11-101192845-G-A
• rs10501973
• ENST00000632820.1:n.1209-2640G>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PGR-AS1	ENST00000632820.1	n.1209-2640G>A		intron_variant	Intron 5 of 6	1
PGR-AS1	ENST00000531772.1	n.181-16498G>A		intron_variant	Intron 2 of 2	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;