chr14-74862615-T-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001243007.2(PROX2):c.1220A>G(p.Glu407Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00402 in 1,613,986 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001243007.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROX2 | NM_001243007.2 | c.1220A>G | p.Glu407Gly | missense_variant | 3/6 | ENST00000556489.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROX2 | ENST00000556489.4 | c.1220A>G | p.Glu407Gly | missense_variant | 3/6 | 1 | NM_001243007.2 | P1 | |
PROX2 | ENST00000673765.1 | c.732+488A>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00346 AC: 526AN: 152172Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00369 AC: 920AN: 249278Hom.: 3 AF XY: 0.00365 AC XY: 494AN XY: 135234
GnomAD4 exome AF: 0.00408 AC: 5967AN: 1461696Hom.: 23 Cov.: 32 AF XY: 0.00404 AC XY: 2940AN XY: 727132
GnomAD4 genome ? AF: 0.00345 AC: 526AN: 152290Hom.: 2 Cov.: 32 AF XY: 0.00349 AC XY: 260AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | PROX2: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 03, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at