ENST00000413560.5:n.394+8254C>G

Variant names:

• chr1-213886409-G-C
• rs723632
• ENST00000413560.5:n.394+8254C>G

Variant summary

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

The ENST00000413560.5(PROX1-AS1):​n.394+8254C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,122 control chromosomes in the GnomAD database, including 44,931 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 0.71 (44931 hom., cov: 32)
• Consequence: PROX1-AS1 ENST00000413560.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413560.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PROX1-AS1	NR_037850.2		n.505+8254C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PROX1-AS1	ENST00000413560.5	TSL:5	n.394+8254C>G		intron	N/A
	PROX1-AS1	ENST00000433082.6	TSL:5	n.482+8254C>G		intron	N/A
	PROX1-AS1	ENST00000593620.5	TSL:5	n.588+8254C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107499 AN: 152004 Hom.: 44940 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.707 AC: 107498 AN: 152122 Hom.: 44931 Cov.: 32 AF XY: 0.707 AC XY: 52563 AN XY: 74360

African (AFR) AF: 0.233 AC: 9660 AN: 41474

American (AMR) AF: 0.757 AC: 11559 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3158 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3798 AN: 5156

South Asian (SAS) AF: 0.733 AC: 3531 AN: 4816

European-Finnish (FIN) AF: 0.914 AC: 9696 AN: 10604

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63343 AN: 68006

Other (OTH) AF: 0.784 AC: 1655 AN: 2112

Alfa AF: 0.722 Hom.: 3091

Bravo AF: 0.679

Asia WGS AF: 0.711 AC: 2472 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs723632; hg19: chr1-214059752;