ENST00000413560.5:n.188+13560T>C

Variant names:

• chr1-213952511-A-G
• rs2075425
• ENST00000413560.5:n.188+13560T>C

Variant summary

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

The ENST00000413560.5(PROX1-AS1):​n.188+13560T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,798 control chromosomes in the GnomAD database, including 20,435 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 0.50 (20435 hom., cov: 31)
• Consequence: PROX1-AS1 ENST00000413560.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 4 publications found

Genes affected

PROX1-AS1 (HGNC:43656): (PROX1 antisense RNA 1)

ENSG00000225233 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PROX1-AS1	NR_037850.2	n.299+13560T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PROX1-AS1	ENST00000413560.5	n.188+13560T>C		intron_variant	Intron 1 of 3	5
PROX1-AS1	ENST00000433082.6	n.276+13560T>C		intron_variant	Intron 2 of 5	5
PROX1-AS1	ENST00000593620.5	n.217+2512T>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76293 AN: 151680 Hom.: 20400 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.503 AC: 76385 AN: 151798 Hom.: 20435 Cov.: 31 AF XY: 0.508 AC XY: 37696 AN XY: 74174

African (AFR) AF: 0.687 AC: 28492 AN: 41448

American (AMR) AF: 0.518 AC: 7899 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1763 AN: 3468

East Asian (EAS) AF: 0.511 AC: 2613 AN: 5114

South Asian (SAS) AF: 0.430 AC: 2056 AN: 4780

European-Finnish (FIN) AF: 0.500 AC: 5284 AN: 10568

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.395 AC: 26779 AN: 67868

Other (OTH) AF: 0.503 AC: 1057 AN: 2102

Alfa AF: 0.436 Hom.: 22228

Bravo AF: 0.515

Asia WGS AF: 0.499 AC: 1735 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.40
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs2075425; hg19: chr1-214125854;