20-62807529-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007346.4(OGFR):c.172-8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_007346.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OGFR | ENST00000290291.10 | c.172-8C>T | splice_region_variant, intron_variant | Intron 1 of 6 | 1 | NM_007346.4 | ENSP00000290291.6 | |||
OGFR | ENST00000370461 | c.-634C>T | 5_prime_UTR_variant | Exon 1 of 5 | 2 | ENSP00000359491.1 | ||||
OGFR | ENST00000450048 | c.-14C>T | 5_prime_UTR_variant | Exon 1 of 4 | 3 | ENSP00000395168.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248002Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134532
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459812Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726078
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at