rs7106686

chr11-101112367-G-A

Variant summary

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

The NM_000926.4(PGR):c.1789+13640C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,996 control chromosomes in the GnomAD database, including 3,254 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 0.19 (3254 hom., cov: 32)
• Consequence: PGR NM_000926.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

Genes affected

PGR (HGNC:8910): (progesterone receptor) This gene encodes a member of the steroid receptor superfamily. The encoded protein mediates the physiological effects of progesterone, which plays a central role in reproductive events associated with the establishment and maintenance of pregnancy. This gene uses two distinct promotors and translation start sites in the first exon to produce several transcript variants, both protein coding and non-protein coding. Two of the isoforms (A and B) are identical except for an additional 165 amino acids found in the N-terminus of isoform B and mediate their own response genes and physiologic effects with little overlap. [provided by RefSeq, Sep 2015]

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 (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGR	NM_000926.4	c.1789+13640C>T		intron_variant		ENST00000325455.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGR	ENST00000325455.10	c.1789+13640C>T		intron_variant		1	NM_000926.4	P1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28457 AN: 151878 Hom.: 3230 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.188 AC: 28532 AN: 151996 Hom.: 3254 Cov.: 32 AF XY: 0.184 AC XY: 13645 AN XY: 74304

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.0649

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.173

Alfa AF: 0.165 Hom.: 400

Bravo AF: 0.200

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.75
Dann	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7106686; hg19: chr11-100983098;