rs8014204

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001243007.2(PROX2):​c.1608+710C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,202 control chromosomes in the GnomAD database, including 33,771 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 0.65 ( 33770 hom., cov: 33)
Exomes 𝑓: 0.50 ( 1 hom. )

Consequence

PROX2
NM_001243007.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.729
Variant links:
Genes affected
PROX2 (HGNC:26715): (prospero homeobox 2) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
YLPM1 (HGNC:17798): (YLP motif containing 1) Enables RNA binding activity. Predicted to be involved in regulation of telomere maintenance. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Located in cytosol and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PROX2NM_001243007.2 linkuse as main transcriptc.1608+710C>T intron_variant ENST00000556489.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PROX2ENST00000556489.4 linkuse as main transcriptc.1608+710C>T intron_variant 1 NM_001243007.2 P1
YLPM1ENST00000554107.2 linkuse as main transcriptc.*749G>A 3_prime_UTR_variant 4/43
PROX2ENST00000673765.1 linkuse as main transcriptc.927+710C>T intron_variant Q3B8N5-2

Frequencies

GnomAD3 genomes
AF:
0.646
AC:
98244
AN:
152072
Hom.:
33725
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.903
Gnomad AMI
AF:
0.578
Gnomad AMR
AF:
0.540
Gnomad ASJ
AF:
0.549
Gnomad EAS
AF:
0.450
Gnomad SAS
AF:
0.674
Gnomad FIN
AF:
0.663
Gnomad MID
AF:
0.554
Gnomad NFE
AF:
0.531
Gnomad OTH
AF:
0.618
GnomAD4 exome
AF:
0.500
AC:
5
AN:
10
Hom.:
1
Cov.:
0
AF XY:
0.500
AC XY:
1
AN XY:
2
show subpopulations
Gnomad4 NFE exome
AF:
0.500
GnomAD4 genome
AF:
0.646
AC:
98343
AN:
152192
Hom.:
33770
Cov.:
33
AF XY:
0.649
AC XY:
48287
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.903
Gnomad4 AMR
AF:
0.540
Gnomad4 ASJ
AF:
0.549
Gnomad4 EAS
AF:
0.451
Gnomad4 SAS
AF:
0.673
Gnomad4 FIN
AF:
0.663
Gnomad4 NFE
AF:
0.531
Gnomad4 OTH
AF:
0.619
Alfa
AF:
0.543
Hom.:
34946
Bravo
AF:
0.644
Asia WGS
AF:
0.616
AC:
2142
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.56
DANN
Benign
0.51

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8014204; hg19: chr14-75322794; API