rs138574644

Positions:

• chr13-48307315-C-A
• chr13-48307315-C-G
• chr13-48307315-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_000321.3(RB1):​c.173C>A​(p.Thr58Asn) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T58I) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RB1 NM_000321.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14595494).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RB1	NM_000321.3	c.173C>A	p.Thr58Asn	missense_variant	2/27	ENST00000267163.6	NP_000312.2
RB1	NM_001407165.1	c.173C>A	p.Thr58Asn	missense_variant	2/27		NP_001394094.1
RB1	NM_001407166.1	c.173C>A	p.Thr58Asn	missense_variant	2/17		NP_001394095.1
RB1	NM_001407167.1	c.173C>A	p.Thr58Asn	missense_variant	2/3		NP_001394096.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RB1	ENST00000267163.6	c.173C>A	p.Thr58Asn	missense_variant	2/27	1	NM_000321.3	ENSP00000267163	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	20
DANN	Benign	0.97
DEOGEN2	Benign	0.30	T;.;.
Eigen	Benign	-0.45
Eigen_PC	Benign	-0.29
FATHMM_MKL	Benign	0.44	N
LIST_S2	Benign	0.61	T;T;T
M_CAP	Benign	0.033	D
MetaRNN	Benign	0.15	T;T;T
MetaSVM	Benign	-0.56	T
MutationAssessor	Benign	0.20	N;.;.
MutationTaster	Benign	0.99	N
PrimateAI	Uncertain	0.55	T
PROVEAN	Benign	0.040	N;.;.
REVEL	Benign	0.11
Sift	Benign	0.21	T;.;.
Sift4G	Uncertain	0.058	T;.;.
Polyphen		0.0040	B;.;.
Vest4		0.44
MutPred		0.36		Gain of catalytic residue at P55 (P = 0.0022);Gain of catalytic residue at P55 (P = 0.0022);Gain of catalytic residue at P55 (P = 0.0022);
MVP		0.68
MPC		0.51
ClinPred		0.22	T
GERP RS		2.7
Varity_R		0.044
gMVP		0.18

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: chr13-48881451;