13-48294399-T-C

Variant names:

• chr13-48294399-T-C
• rs9568029
• ENST00000718572.1:n.393-2504A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000718572.1(RB1-DT):​n.393-2504A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,044 control chromosomes in the GnomAD database, including 29,055 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 0.57 (29055 hom., cov: 32)
• Consequence: RB1-DT ENST00000718572.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 5 publications found

Genes affected

RB1-DT (HGNC:42778): (RB1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718572.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RB1-DT	ENST00000718572.1		n.393-2504A>G		intron	N/A
	RB1-DT	ENST00000718573.1		n.552-2504A>G		intron	N/A
	RB1-DT	ENST00000718574.1		n.356-2504A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87021 AN: 151926 Hom.: 29061 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.572 AC: 87023 AN: 152044 Hom.: 29055 Cov.: 32 AF XY: 0.575 AC XY: 42723 AN XY: 74310

African (AFR) AF: 0.199 AC: 8235 AN: 41462

American (AMR) AF: 0.696 AC: 10637 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2520 AN: 3470

East Asian (EAS) AF: 0.698 AC: 3602 AN: 5164

South Asian (SAS) AF: 0.615 AC: 2965 AN: 4822

European-Finnish (FIN) AF: 0.727 AC: 7678 AN: 10560

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49291 AN: 67970

Other (OTH) AF: 0.611 AC: 1293 AN: 2116

Alfa AF: 0.505 Hom.: 1927

Bravo AF: 0.555

Asia WGS AF: 0.573 AC: 1998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.69
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs9568029; hg19: chr13-48868535;