chr15-28018482-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000275.3(OCA2):c.722C>T(p.Pro241Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,470 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P241R) has been classified as Benign.
Frequency
Consequence
NM_000275.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OCA2 | NM_000275.3 | c.722C>T | p.Pro241Leu | missense_variant | 7/24 | ENST00000354638.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OCA2 | ENST00000354638.8 | c.722C>T | p.Pro241Leu | missense_variant | 7/24 | 1 | NM_000275.3 | P1 | |
OCA2 | ENST00000353809.9 | c.722C>T | p.Pro241Leu | missense_variant | 7/23 | 1 | |||
OCA2 | ENST00000431101.1 | c.722C>T | p.Pro241Leu | missense_variant | 7/7 | 3 | |||
OCA2 | ENST00000445578.5 | c.574-2296C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000442 AC: 11AN: 248756Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135078
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461292Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 726970
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at