rs17762150

Variant names:

• chr1-213951475-C-T
• rs17762150
• ENST00000413560.5:n.188+14596G>A

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+14596G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,028 control chromosomes in the GnomAD database, including 10,971 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 0.37 (10971 hom., cov: 33)
• Consequence: PROX1-AS1 ENST00000413560.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PROX1-AS1	NR_037850.2	n.299+14596G>A		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+14596G>A		intron_variant	Intron 1 of 3	5
PROX1-AS1	ENST00000433082.6	n.276+14596G>A		intron_variant	Intron 2 of 5	5
PROX1-AS1	ENST00000593620.5	n.217+3548G>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56408 AN: 151910 Hom.: 10971 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.371 AC: 56418 AN: 152028 Hom.: 10971 Cov.: 33 AF XY: 0.374 AC XY: 27785 AN XY: 74304

African (AFR) AF: 0.280 AC: 11617 AN: 41486

American (AMR) AF: 0.370 AC: 5652 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1690 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1078 AN: 5176

South Asian (SAS) AF: 0.238 AC: 1146 AN: 4812

European-Finnish (FIN) AF: 0.519 AC: 5474 AN: 10548

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28428 AN: 67936

Other (OTH) AF: 0.421 AC: 890 AN: 2114

Alfa AF: 0.387 Hom.: 2260

Bravo AF: 0.361

Asia WGS AF: 0.255 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.77
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17762150; hg19: chr1-214124818;