chr1-213997437-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001270616.2(PROX1):c.902A>G(p.Glu301Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000431 in 1,614,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E301K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001270616.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROX1 | NM_001270616.2 | c.902A>G | p.Glu301Gly | missense_variant | 2/5 | ENST00000366958.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROX1 | ENST00000366958.9 | c.902A>G | p.Glu301Gly | missense_variant | 2/5 | 1 | NM_001270616.2 | P1 | |
PROX1 | ENST00000435016.2 | c.902A>G | p.Glu301Gly | missense_variant | 2/5 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000294 AC: 74AN: 251410Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135888
GnomAD4 exome AF: 0.000458 AC: 669AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.000428 AC XY: 311AN XY: 727234
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.902A>G (p.E301G) alteration is located in exon 2 (coding exon 1) of the PROX1 gene. This alteration results from a A to G substitution at nucleotide position 902, causing the glutamic acid (E) at amino acid position 301 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at