13-48302221-C-A

Variant names:

• chr13-48302221-C-A
• rs1573601
• ENST00000433480.4:n.587+118G>T

Variant summary

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

The ENST00000433480.4(RB1-DT):​n.587+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 ENST00000433480.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 8 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433480.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RB1-DT	NR_046414.2		n.566+118G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RB1-DT	ENST00000433480.4	TSL:1	n.587+118G>T		intron	N/A
	RB1-DT	ENST00000718582.1		n.705G>T		non_coding_transcript_exon	Exon 2 of 2
	RB1-DT	ENST00000718583.1		n.508G>T		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.278 AC: 5 AN: 18

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.116 AC: 4823 AN: 41568

American (AMR) AF: 0.174 AC: 2658 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 695 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1168 AN: 5186

South Asian (SAS) AF: 0.237 AC: 1143 AN: 4826

European-Finnish (FIN) AF: 0.265 AC: 2810 AN: 10586

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16758 AN: 67992

Other (OTH) AF: 0.196 AC: 415 AN: 2114

Alfa AF: 0.224 Hom.: 3437

Bravo AF: 0.194

Asia WGS AF: 0.221 AC: 765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.78
DANN	Benign	0.65
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs1573601; hg19: chr13-48876357;