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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PGR-AS1	ENST00000843145.1	n.574-81982T>C		intron_variant	Intron 5 of 6
PGR-AS1	ENST00000843146.1	n.264-81982T>C		intron_variant	Intron 2 of 3
PGR-AS1	ENST00000843147.1	n.533-81982T>C		intron_variant	Intron 5 of 5
PGR-AS1	ENST00000843148.1	n.98-81982T>C		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs2156522; hg19: chr11-101112647;