dbSNP rs1573601: RB1-DT:n.587+118G>T (chr13-48302221-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.599

Publications

8 publications found

Variant links:

Genes affected

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

RB1-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RB1-DT	NR_046414.2 link	n.566+118G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
RB1-DT	ENST00000433480.4 link	n.587+118G>T	intron_variant	Intron 2 of 2	1
RB1-DT	ENST00000718582.1 link	n.705G>T	non_coding_transcript_exon_variant	Exon 2 of 2
RB1-DT	ENST00000718583.1 link	n.508G>T	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30827

AN:

152136

Hom.:

3381

Cov.:

show subpopulations

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:

AN:

Hom.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.278

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.202

AC:

30821

AN:

152254

Hom.:

3376

Cov.:

AF XY:

0.205

AC XY:

15262

AN XY:

74428

show subpopulations

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:

AN:

292

European-Non Finnish (NFE)

AF:

0.246

AC:

16758

AN:

67992

Other (OTH)

AF:

0.196

AC:

415

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1267

2535

3802

5070

6337

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

346

692

1038

1384

1730

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.78

(source)

DANN

Benign

0.65

PhyloP100

-0.60

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over