rs10501973

Variant names:

• chr11-101192845-G-A
• rs10501973
• ENST00000632820.1:n.1209-2640G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000632820.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGR-AS1	ENST00000632820.1	TSL:1	n.1209-2640G>A		intron	N/A
	PGR-AS1	ENST00000531772.2	TSL:2	n.524-16498G>A		intron	N/A
	PGR-AS1	ENST00000843145.1		n.573+33590G>A		intron	N/A

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

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: 27 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: 64 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19553 AN: 67866

Other (OTH) AF: 0.195 AC: 411 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.41
PhyloP100		0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10501973;

hg19: chr11-101063576;