chr11-101265124-C-T

Variant names:

• chr11-101265124-C-T
• rs1943753
• ENST00000843145.1:n.574-58774C>T

Variant summary

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

The ENST00000843145.1(PGR-AS1):​n.574-58774C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0904 in 152,008 control chromosomes in the GnomAD database, including 738 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 0.090 (738 hom., cov: 32)
• Consequence: PGR-AS1 ENST00000843145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.122 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.574-58774C>T		intron_variant	Intron 5 of 6
PGR-AS1	ENST00000843146.1	n.264-58774C>T		intron_variant	Intron 2 of 3
PGR-AS1	ENST00000843147.1	n.533-58774C>T		intron_variant	Intron 5 of 5
PGR-AS1	ENST00000843148.1	n.98-58774C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0904 AC: 13724 AN: 151890 Hom.: 737 Cov.: 32

Gnomad AFR AF: 0.0508

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0675

Gnomad EAS AF: 0.000967

Gnomad SAS AF: 0.0873

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.0904 AC: 13737 AN: 152008 Hom.: 738 Cov.: 32 AF XY: 0.0912 AC XY: 6774 AN XY: 74302

African (AFR) AF: 0.0511 AC: 2119 AN: 41476

American (AMR) AF: 0.126 AC: 1927 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0675 AC: 234 AN: 3468

East Asian (EAS) AF: 0.000969 AC: 5 AN: 5160

South Asian (SAS) AF: 0.0872 AC: 420 AN: 4816

European-Finnish (FIN) AF: 0.0851 AC: 898 AN: 10552

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7854 AN: 67956

Other (OTH) AF: 0.0893 AC: 189 AN: 2116

Alfa AF: 0.103 Hom.: 176

Bravo AF: 0.0909

Asia WGS AF: 0.0460 AC: 159 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	2.0
DANN	Benign	0.18
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1943753; hg19: chr11-101135855;