chr8-86629043-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_019098.5(CNGB3):c.1356G>A(p.Gln452Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00965 in 1,613,948 control chromosomes in the GnomAD database, including 1,272 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_019098.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNGB3 | ENST00000320005.6 | c.1356G>A | p.Gln452Gln | synonymous_variant | Exon 12 of 18 | 1 | NM_019098.5 | ENSP00000316605.5 | ||
CNGB3 | ENST00000681546.1 | n.1176G>A | non_coding_transcript_exon_variant | Exon 7 of 13 | ||||||
CNGB3 | ENST00000681746.1 | n.1356G>A | non_coding_transcript_exon_variant | Exon 12 of 19 | ENSP00000505959.1 |
Frequencies
GnomAD3 genomes AF: 0.0514 AC: 7810AN: 152076Hom.: 675 Cov.: 32
GnomAD3 exomes AF: 0.0139 AC: 3492AN: 250978Hom.: 269 AF XY: 0.0103 AC XY: 1397AN XY: 135606
GnomAD4 exome AF: 0.00529 AC: 7738AN: 1461752Hom.: 595 Cov.: 32 AF XY: 0.00454 AC XY: 3301AN XY: 727180
GnomAD4 genome AF: 0.0515 AC: 7837AN: 152196Hom.: 677 Cov.: 32 AF XY: 0.0489 AC XY: 3643AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:3
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not provided Benign:3
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Achromatopsia Benign:1
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Severe early-childhood-onset retinal dystrophy Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Achromatopsia 3 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at