chr3-87259897-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000306.4(POU1F1):c.873A>G(p.Arg291=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000385 in 1,612,306 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R291R) has been classified as Likely benign.
Frequency
Consequence
NM_000306.4 synonymous
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 |
---|---|---|---|---|---|---|---|
POU1F1 | NM_000306.4 | c.873A>G | p.Arg291= | synonymous_variant | 6/6 | ENST00000350375.7 | |
POU1F1 | NM_001122757.3 | c.951A>G | p.Arg317= | synonymous_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU1F1 | ENST00000350375.7 | c.873A>G | p.Arg291= | synonymous_variant | 6/6 | 1 | NM_000306.4 | P4 | |
POU1F1 | ENST00000344265.8 | c.951A>G | p.Arg317= | synonymous_variant | 6/6 | 5 | A1 | ||
POU1F1 | ENST00000561167.5 | c.648A>G | p.Arg216= | synonymous_variant | 5/5 | 5 | |||
POU1F1 | ENST00000560656.1 | c.*137A>G | 3_prime_UTR_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250364Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135522
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1460072Hom.: 0 Cov.: 31 AF XY: 0.0000427 AC XY: 31AN XY: 726508
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at