11-101095907-T-A

Position:

• chr11-101095907-T-A

Variant summary

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

The NM_000926.4(PGR):​c.1790-4031A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,068 control chromosomes in the GnomAD database, including 40,472 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 0.71 (40472 hom., cov: 32)
• Consequence: PGR NM_000926.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGR	NM_000926.4	c.1790-4031A>T		intron_variant		ENST00000325455.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGR	ENST00000325455.10	c.1790-4031A>T		intron_variant		1	NM_000926.4	P1

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108572 AN: 151950 Hom.: 40446 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.714 AC: 108641 AN: 152068 Hom.: 40472 Cov.: 32 AF XY: 0.707 AC XY: 52604 AN XY: 74354

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.710

Alfa AF: 0.731 Hom.: 2654

Bravo AF: 0.700

Asia WGS AF: 0.374 AC: 1304 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.63

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: rs542384; hg19: chr11-100966638;