GeneBe

rs2075423

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000598091.1(PROX1-AS1):​n.88C>T variant causes a non coding transcript exon change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 24)

Consequence

PROX1-AS1
ENST00000598091.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.73
Variant links:
Genes affected
PROX1-AS1 (HGNC:43656): (PROX1 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PROX1-AS1NR_037850.2 linkn.85+4693C>T intron_variant Intron 1 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PROX1-AS1ENST00000598091.1 linkn.88C>T non_coding_transcript_exon_variant Exon 2 of 5 5
PROX1-AS1ENST00000630180.2 linkn.135C>T non_coding_transcript_exon_variant Exon 2 of 8 5
PROX1-AS1ENST00000433082.6 linkn.62+6945C>T intron_variant Intron 1 of 5 5

Frequencies

GnomAD3 genomes
Cov.:
24
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
11
DANN
Benign
0.62

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-214154719; API