chr5-93740908-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153216.2(POU5F2):c.656G>A(p.Arg219Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153216.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POU5F2 | NM_153216.2 | c.656G>A | p.Arg219Gln | missense_variant | 1/1 | ENST00000606183.4 | |
FAM172A | NM_032042.6 | c.1108+35251G>A | intron_variant | ENST00000395965.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU5F2 | ENST00000606183.4 | c.656G>A | p.Arg219Gln | missense_variant | 1/1 | NM_153216.2 | P1 | ||
FAM172A | ENST00000395965.8 | c.1108+35251G>A | intron_variant | 1 | NM_032042.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000361 AC: 55AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000722 AC: 18AN: 249256Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135214
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461706Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727134
GnomAD4 genome ? AF: 0.000361 AC: 55AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.000417 AC XY: 31AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 26, 2022 | The c.656G>A (p.R219Q) alteration is located in exon 1 (coding exon 1) of the POU5F2 gene. This alteration results from a G to A substitution at nucleotide position 656, causing the arginine (R) at amino acid position 219 to be replaced by a glutamine (Q). 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