rs200501806
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000321.3(RB1):c.1961-6C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000321.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RB1 | NM_000321.3 | c.1961-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000267163.6 | NP_000312.2 | |||
RB1 | NM_001407165.1 | c.1961-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_001394094.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RB1 | ENST00000267163.6 | c.1961-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000321.3 | ENSP00000267163 | P1 | |||
RB1 | ENST00000643064.1 | c.194+78239C>A | intron_variant | ENSP00000496005 | ||||||
RB1 | ENST00000650461.1 | c.1961-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENSP00000497193 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251442Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135914
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461798Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727200
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
Retinoblastoma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at