14-74863502-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_001243007.2(PROX2):c.333G>A(p.Pro111=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00393 in 1,613,302 control chromosomes in the GnomAD database, including 194 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.020 ( 95 hom., cov: 32)
Exomes 𝑓: 0.0022 ( 99 hom. )
Consequence
PROX2
NM_001243007.2 synonymous
NM_001243007.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.473
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 14-74863502-C-T is Benign according to our data. Variant chr14-74863502-C-T is described in ClinVar as [Benign]. Clinvar id is 783693.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.473 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0671 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROX2 | NM_001243007.2 | c.333G>A | p.Pro111= | synonymous_variant | 3/6 | ENST00000556489.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROX2 | ENST00000556489.4 | c.333G>A | p.Pro111= | synonymous_variant | 3/6 | 1 | NM_001243007.2 | P1 | |
PROX2 | ENST00000673765.1 | c.333G>A | p.Pro111= | synonymous_variant | 3/5 |
Frequencies
GnomAD3 genomes AF: 0.0201 AC: 3055AN: 152222Hom.: 94 Cov.: 32
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GnomAD3 exomes AF: 0.00535 AC: 1323AN: 247298Hom.: 49 AF XY: 0.00409 AC XY: 549AN XY: 134186
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GnomAD4 exome AF: 0.00224 AC: 3276AN: 1460962Hom.: 99 Cov.: 32 AF XY: 0.00201 AC XY: 1457AN XY: 726678
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GnomAD4 genome AF: 0.0201 AC: 3061AN: 152340Hom.: 95 Cov.: 32 AF XY: 0.0193 AC XY: 1435AN XY: 74498
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 18, 2018 | - - |
Computational scores
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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