rs1367951

Variant names:

• chr1-213952170-A-G
• rs1367951
• ENST00000413560.5:n.188+13901T>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+13901T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,972 control chromosomes in the GnomAD database, including 11,859 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 0.39 (11859 hom., cov: 32)
• Consequence: PROX1-AS1 ENST00000413560.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 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.299+13901T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PROX1-AS1	ENST00000413560.5	TSL:5	n.188+13901T>C		intron	N/A
	PROX1-AS1	ENST00000433082.6	TSL:5	n.276+13901T>C		intron	N/A
	PROX1-AS1	ENST00000593620.5	TSL:5	n.217+2853T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59135 AN: 151854 Hom.: 11854 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.389 AC: 59158 AN: 151972 Hom.: 11859 Cov.: 32 AF XY: 0.392 AC XY: 29119 AN XY: 74278

African (AFR) AF: 0.341 AC: 14116 AN: 41444

American (AMR) AF: 0.382 AC: 5829 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1691 AN: 3466

East Asian (EAS) AF: 0.204 AC: 1052 AN: 5156

South Asian (SAS) AF: 0.238 AC: 1146 AN: 4822

European-Finnish (FIN) AF: 0.518 AC: 5468 AN: 10558

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28501 AN: 67934

Other (OTH) AF: 0.432 AC: 911 AN: 2110

Alfa AF: 0.409 Hom.: 3198

Bravo AF: 0.382

Asia WGS AF: 0.258 AC: 900 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	8.8
DANN	Benign	0.78
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1367951; hg19: chr1-214125513;