rs530961288
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_Very_StrongBP7BS2_Supporting
The NM_000321.3(RB1):āc.30C>Gā(p.Ala10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000146 in 1,509,364 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. A10A) has been classified as Likely benign.
Frequency
Consequence
NM_000321.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RB1 | NM_000321.3 | c.30C>G | p.Ala10= | synonymous_variant | 1/27 | ENST00000267163.6 | |
RB1 | NM_001407165.1 | c.30C>G | p.Ala10= | synonymous_variant | 1/27 | ||
RB1 | NM_001407166.1 | c.30C>G | p.Ala10= | synonymous_variant | 1/17 | ||
RB1 | NM_001407167.1 | c.30C>G | p.Ala10= | synonymous_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RB1 | ENST00000267163.6 | c.30C>G | p.Ala10= | synonymous_variant | 1/27 | 1 | NM_000321.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 151884Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000125 AC: 17AN: 1357376Hom.: 0 Cov.: 31 AF XY: 0.0000119 AC XY: 8AN XY: 669576
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 151988Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74314
ClinVar
Submissions by phenotype
Retinoblastoma Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Nov 30, 2023 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2019 | 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