chrX-154154684-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020061.6(OPN1LW):c.689T>C(p.Ile230Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00296 in 1,188,737 control chromosomes in the GnomAD database, including 10 homozygotes. There are 191 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_020061.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPN1LW | NM_020061.6 | c.689T>C | p.Ile230Thr | missense_variant | 4/6 | ENST00000369951.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPN1LW | ENST00000369951.9 | c.689T>C | p.Ile230Thr | missense_variant | 4/6 | 1 | NM_020061.6 | P1 | |
OPN1LW | ENST00000442922.1 | c.278T>C | p.Ile93Thr | missense_variant | 2/4 | 5 | |||
OPN1LW | ENST00000463296.1 | n.588+1576T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00244 AC: 260AN: 106704Hom.: 0 Cov.: 17 AF XY: 0.000303 AC XY: 9AN XY: 29692
GnomAD3 exomes AF: 0.00232 AC: 418AN: 180224Hom.: 3 AF XY: 0.000461 AC XY: 30AN XY: 65072
GnomAD4 exome AF: 0.00301 AC: 3253AN: 1081981Hom.: 10 Cov.: 31 AF XY: 0.000522 AC XY: 182AN XY: 348799
GnomAD4 genome ? AF: 0.00244 AC: 260AN: 106756Hom.: 0 Cov.: 17 AF XY: 0.000302 AC XY: 9AN XY: 29754
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | OPN1LW: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at