20-62812373-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007346.4(OGFR):c.758C>T(p.Ala253Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000771 in 1,569,512 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 (★).
Frequency
Consequence
NM_007346.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OGFR | ENST00000290291.10 | c.758C>T | p.Ala253Val | missense_variant | Exon 7 of 7 | 1 | NM_007346.4 | ENSP00000290291.6 | ||
OGFR | ENST00000370461.5 | c.602C>T | p.Ala201Val | missense_variant | Exon 5 of 5 | 2 | ENSP00000359491.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000503 AC: 9AN: 179102Hom.: 0 AF XY: 0.0000515 AC XY: 5AN XY: 97018
GnomAD4 exome AF: 0.0000790 AC: 112AN: 1417320Hom.: 0 Cov.: 63 AF XY: 0.0000784 AC XY: 55AN XY: 701626
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.758C>T (p.A253V) alteration is located in exon 7 (coding exon 7) of the OGFR gene. This alteration results from a C to T substitution at nucleotide position 758, causing the alanine (A) at amino acid position 253 to be replaced by a valine (V). 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