Genetic Variant RORB-AS1:n.858-2600C>G (chr9-74126500-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000715876.1(RORB-AS1):n.858-2600C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,034 control chromosomes in the GnomAD database, including 3,964 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 0.21 ( 3964 hom., cov: 32)

Consequence

RORB-AS1
ENST00000715876.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.106

Publications

2 publications found

Variant links:

COSMIC-nc: COSV60360500

Genes affected

RORB-AS1 (HGNC:49803): (RORB antisense RNA 1)

RORB-AS1 links:

LOC101927329 (HGNC:):

LOC101927329 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927329	XR_242624.4 link	n.686-2600C>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
RORB-AS1	ENST00000715876.1 link	n.858-2600C>G	intron_variant	Intron 5 of 5
RORB-AS1	ENST00000722221.1 link	n.687-2600C>G	intron_variant	Intron 4 of 4
RORB-AS1	ENST00000722222.1 link	n.955-2600C>G	intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31387

AN:

151916

Hom.:

3970

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0750

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.312

Gnomad EAS

AF:

0.459

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.239

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

GnomAD4 genome

AF:

0.206

AC:

31381

AN:

152034

Hom.:

3964

Cov.:

AF XY:

0.210

AC XY:

15603

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.0750

AC:

3111

AN:

41482

American (AMR)

AF:

0.318

AC:

4851

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.312

AC:

1081

AN:

3466

East Asian (EAS)

AF:

0.459

AC:

2371

AN:

5164

South Asian (SAS)

AF:

0.347

AC:

1669

AN:

4814

European-Finnish (FIN)

AF:

0.170

AC:

1790

AN:

10538

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.230

AC:

15636

AN:

67976

Other (OTH)

AF:

0.236

AC:

498

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1214

2428

3642

4856

6070

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.209

Hom.:

473

Bravo

AF:

0.213

Asia WGS

AF:

0.349

AC:

1213

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.7

(source)

DANN

Benign

0.51

PhyloP100

0.11

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over