19-49035617-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_033377.2(CGB1):c.461G>A(p.Gly154Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,611,406 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_033377.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CGB1 | ENST00000301407.8 | c.461G>A | p.Gly154Glu | missense_variant | Exon 3 of 3 | 1 | NM_033377.2 | ENSP00000301407.6 | ||
ENSG00000267335 | ENST00000591656.1 | c.-28+909G>A | intron_variant | Intron 1 of 2 | 2 | ENSP00000466140.1 | ||||
ENSG00000267335 | ENST00000604577.1 | c.9+1086G>A | intron_variant | Intron 1 of 2 | 1 | ENSP00000474022.1 | ||||
CGB1 | ENST00000601167.1 | c.*36G>A | downstream_gene_variant | 5 | ENSP00000472896.2 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151620Hom.: 0 Cov.: 27
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250958Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135830
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1459786Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 8AN XY: 726192
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151620Hom.: 0 Cov.: 27 AF XY: 0.0000270 AC XY: 2AN XY: 74056
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at