chr7-5882494-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001097622.2(OCM):āc.63C>Gā(p.Asp21Glu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,614,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001097622.2 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
OCM | NM_001097622.2 | c.63C>G | p.Asp21Glu | missense_variant, splice_region_variant | 2/4 | ENST00000242104.6 | |
OCM | NM_001391990.1 | c.63C>G | p.Asp21Glu | missense_variant, splice_region_variant | 3/5 | ||
OCM | NM_001391991.1 | c.-52C>G | splice_region_variant, 5_prime_UTR_variant | 2/4 | |||
OCM | XM_047420752.1 | c.-52C>G | splice_region_variant, 5_prime_UTR_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OCM | ENST00000242104.6 | c.63C>G | p.Asp21Glu | missense_variant, splice_region_variant | 2/4 | 1 | NM_001097622.2 | P1 | |
OCM | ENST00000416608.5 | c.63C>G | p.Asp21Glu | missense_variant, splice_region_variant | 3/5 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152166Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251400Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135878
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461752Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727170
GnomAD4 genome AF: 0.000138 AC: 21AN: 152284Hom.: 0 Cov.: 31 AF XY: 0.000107 AC XY: 8AN XY: 74462
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at