5-93740905-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153216.2(POU5F2):c.659G>C(p.Arg220Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R220Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_153216.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POU5F2 | NM_153216.2 | c.659G>C | p.Arg220Pro | missense_variant | Exon 1 of 1 | ENST00000606183.4 | NP_694948.1 | |
ARB2A | NM_032042.6 | c.1108+35254G>C | intron_variant | Intron 10 of 10 | ENST00000395965.8 | NP_114431.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POU5F2 | ENST00000606183.4 | c.659G>C | p.Arg220Pro | missense_variant | Exon 1 of 1 | 6 | NM_153216.2 | ENSP00000489796.1 | ||
FAM172A | ENST00000395965.8 | c.1108+35254G>C | intron_variant | Intron 10 of 10 | 1 | NM_032042.6 | ENSP00000379294.3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249262Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135220
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461708Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727136
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.659G>C (p.R220P) alteration is located in exon 1 (coding exon 1) of the POU5F2 gene. This alteration results from a G to C substitution at nucleotide position 659, causing the arginine (R) at amino acid position 220 to be replaced by a proline (P). 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