rs1573601

Positions:

• chr13-48302221-C-A
• chr13-48302221-C-G

Variant summary

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

The ENST00000433480.3(RB1-DT):​n.566+118G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,276 control chromosomes in the GnomAD database, including 3,377 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 0.20 (3376 hom., cov: 32)
  • Exomes 𝑓: 0.23 (1 hom.)
• Consequence: RB1-DT ENST00000433480.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

Genes affected

RB1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RB1-DT	NR_046414.2	n.566+118G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RB1-DT	ENST00000433480.3	n.566+118G>T		intron_variant		1
RB1-DT	ENST00000436963.2	n.345+118G>T		intron_variant		3
RB1-DT	ENST00000669900.1	n.353+118G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30827 AN: 152136 Hom.: 3381 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.227 AC: 5 AN: 22 Hom.: 1 AF XY: 0.167 AC XY: 3 AN XY: 18

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.278

GnomAD4 genome AF: 0.202 AC: 30821 AN: 152254 Hom.: 3376 Cov.: 32 AF XY: 0.205 AC XY: 15262 AN XY: 74428

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.196

Alfa AF: 0.232 Hom.: 2581

Bravo AF: 0.194

Asia WGS AF: 0.221 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.78
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1573601; hg19: chr13-48876357;