13-48345161-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_000321.3(RB1):​c.462G>C​(p.Lys154Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

RB1
NM_000321.3 missense

Scores

2
8
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.625
Variant links:
Genes affected
RB1 (HGNC:9884): (RB transcriptional corepressor 1) The protein encoded by this gene is a negative regulator of the cell cycle and was the first tumor suppressor gene found. The encoded protein also stabilizes constitutive heterochromatin to maintain the overall chromatin structure. The active, hypophosphorylated form of the protein binds transcription factor E2F1. Defects in this gene are a cause of childhood cancer retinoblastoma (RB), bladder cancer, and osteogenic sarcoma. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.36552683).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RB1NM_000321.3 linkc.462G>C p.Lys154Asn missense_variant Exon 4 of 27 ENST00000267163.6 NP_000312.2 P06400A0A024RDV3
RB1NM_001407165.1 linkc.462G>C p.Lys154Asn missense_variant Exon 4 of 27 NP_001394094.1
RB1NM_001407166.1 linkc.462G>C p.Lys154Asn missense_variant Exon 4 of 17 NP_001394095.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RB1ENST00000267163.6 linkc.462G>C p.Lys154Asn missense_variant Exon 4 of 27 1 NM_000321.3 ENSP00000267163.4 P06400
RB1ENST00000467505.5 linkn.138-14856G>C intron_variant Intron 1 of 2 1 ENSP00000434702.1 Q92728
RB1ENST00000650461.1 linkc.462G>C p.Lys154Asn missense_variant Exon 4 of 27 ENSP00000497193.1 A0A3B3IS71
RB1ENST00000525036.1 linkn.624G>C non_coding_transcript_exon_variant Exon 4 of 7 3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.82
BayesDel_addAF
Benign
-0.062
T
BayesDel_noAF
Benign
-0.33
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.36
T;.
Eigen
Uncertain
0.31
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Benign
0.71
D
LIST_S2
Uncertain
0.89
D;D
M_CAP
Uncertain
0.10
D
MetaRNN
Benign
0.37
T;T
MetaSVM
Benign
-0.44
T
MutationAssessor
Uncertain
2.4
M;.
PrimateAI
Uncertain
0.63
T
PROVEAN
Benign
-1.3
N;.
REVEL
Uncertain
0.39
Sift
Benign
0.56
T;.
Sift4G
Pathogenic
0.0
D;.
Polyphen
1.0
D;.
Vest4
0.59
MutPred
0.64
Gain of ubiquitination at K153 (P = 0.0356);Gain of ubiquitination at K153 (P = 0.0356);
MVP
0.88
MPC
1.4
ClinPred
0.93
D
GERP RS
2.8
Varity_R
0.20
gMVP
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr13-48919297; API