11-101241916-T-C

Variant names:

• chr11-101241916-T-C
• rs2156522
• ENST00000843145.1:n.574-81982T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000843145.1(PGR-AS1):​n.574-81982T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,206 control chromosomes in the GnomAD database, including 6,121 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 0.24 (6121 hom., cov: 33)
• Consequence: PGR-AS1 ENST00000843145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843145.1. 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	ENST00000843145.1		n.574-81982T>C		intron	N/A
	PGR-AS1	ENST00000843146.1		n.264-81982T>C		intron	N/A
	PGR-AS1	ENST00000843147.1		n.533-81982T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37169 AN: 152088 Hom.: 6120 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.244 AC: 37184 AN: 152206 Hom.: 6121 Cov.: 33 AF XY: 0.252 AC XY: 18760 AN XY: 74414

African (AFR) AF: 0.298 AC: 12384 AN: 41544

American (AMR) AF: 0.266 AC: 4075 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3472

East Asian (EAS) AF: 0.881 AC: 4560 AN: 5176

South Asian (SAS) AF: 0.398 AC: 1921 AN: 4822

European-Finnish (FIN) AF: 0.198 AC: 2095 AN: 10584

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10905 AN: 67990

Other (OTH) AF: 0.221 AC: 467 AN: 2112

Alfa AF: 0.202 Hom.: 464

Bravo AF: 0.254

Asia WGS AF: 0.581 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-1.1

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: rs2156522;

hg19: chr11-101112647;