rs7329938

Positions:

• chr13-48357843-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000321.3(RB1):​c.608-2174T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0782 in 152,234 control chromosomes in the GnomAD database, including 637 homozygotes. 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: 𝑓 0.078 (637 hom., cov: 32)
• Consequence: RB1 NM_000321.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

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]

RB1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RB1	NM_000321.3	c.608-2174T>C		intron_variant		ENST00000267163.6	NP_000312.2
RB1	NM_001407165.1	c.608-2174T>C		intron_variant			NP_001394094.1
RB1	NM_001407166.1	c.608-2174T>C		intron_variant			NP_001394095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RB1	ENST00000267163.6	c.608-2174T>C		intron_variant		1	NM_000321.3	ENSP00000267163.4
RB1	ENST00000467505.5	n.138-2174T>C		intron_variant		1		ENSP00000434702.1
RB1	ENST00000650461.1	c.608-2174T>C		intron_variant				ENSP00000497193.1
RB1	ENST00000525036.1	n.770-2174T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0783 AC: 11911 AN: 152116 Hom.: 638 Cov.: 32

Gnomad AFR AF: 0.0204

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.0337

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0731

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0833

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0782 AC: 11903 AN: 152234 Hom.: 637 Cov.: 32 AF XY: 0.0774 AC XY: 5758 AN XY: 74430

Gnomad4 AFR AF: 0.0204

Gnomad4 AMR AF: 0.0646

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.0334

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0731

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0819

Alfa AF: 0.108 Hom.: 322

Bravo AF: 0.0747

Asia WGS AF: 0.0920 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.6
DANN	Benign	0.91

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

LitVar

Other links and lift over

dbSNP: rs7329938; hg19: chr13-48931979;