11-101192200-G-A

Position:

• chr11-101192200-G-A

Variant summary

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

The variant allele was found at a frequency of 0.447 in 151,850 control chromosomes in the GnomAD database, including 16,551 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 0.45 (16551 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

Genes affected

PGR-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.101192200G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGR-AS1	ENST00000632820.1	n.1209-3285G>A		intron_variant		1
PGR-AS1	ENST00000531772.1	n.181-17143G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67867 AN: 151732 Hom.: 16544 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.00753

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.447 AC: 67891 AN: 151850 Hom.: 16551 Cov.: 32 AF XY: 0.441 AC XY: 32759 AN XY: 74210

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.00754

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.448

Alfa AF: 0.529 Hom.: 9514

Bravo AF: 0.435

Asia WGS AF: 0.185 AC: 645 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.82
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs954723; hg19: chr11-101062931;