chr14-74855624-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001243007.2(PROX2):c.1609-322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 213,920 control chromosomes in the GnomAD database, including 34,559 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 0.58 ( 25948 hom., cov: 34)
Exomes 𝑓: 0.52 ( 8611 hom. )
Consequence
PROX2
NM_001243007.2 intron
NM_001243007.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.685
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=-0.78).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROX2 | NM_001243007.2 | c.1609-322T>C | intron_variant | ENST00000556489.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROX2 | ENST00000556489.4 | c.1609-322T>C | intron_variant | 1 | NM_001243007.2 | P1 | |||
YLPM1 | ENST00000554107.2 | c.*282A>G | 3_prime_UTR_variant | 4/4 | 3 | ||||
PROX2 | ENST00000673765.1 | c.928-322T>C | intron_variant | ||||||
YLPM1 | ENST00000553381.1 | n.645A>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.575 AC: 87498AN: 152052Hom.: 25911 Cov.: 34
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GnomAD4 exome AF: 0.524 AC: 32368AN: 61750Hom.: 8611 Cov.: 0 AF XY: 0.524 AC XY: 16358AN XY: 31216
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GnomAD4 genome ? AF: 0.576 AC: 87585AN: 152170Hom.: 25948 Cov.: 34 AF XY: 0.578 AC XY: 42989AN XY: 74394
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at