9-74282154-A-G

Variant names:

• chr9-74282154-A-G
• rs4013967
• ENST00000715877.1:n.843-190T>C

Variant summary

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

The ENST00000715877.1(RORB-AS1):​n.843-190T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,972 control chromosomes in the GnomAD database, including 34,104 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 0.64 (34104 hom., cov: 31)
• Consequence: RORB-AS1 ENST00000715877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 10 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715877.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RORB-AS1	ENST00000715877.1		n.843-190T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97106 AN: 151854 Hom.: 34089 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.639 AC: 97152 AN: 151972 Hom.: 34104 Cov.: 31 AF XY: 0.648 AC XY: 48128 AN XY: 74290

African (AFR) AF: 0.325 AC: 13429 AN: 41382

American (AMR) AF: 0.757 AC: 11556 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2647 AN: 3466

East Asian (EAS) AF: 0.997 AC: 5155 AN: 5168

South Asian (SAS) AF: 0.832 AC: 4012 AN: 4824

European-Finnish (FIN) AF: 0.753 AC: 7950 AN: 10554

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50103 AN: 68000

Other (OTH) AF: 0.692 AC: 1463 AN: 2114

Alfa AF: 0.625 Hom.: 4820

Bravo AF: 0.624

Asia WGS AF: 0.864 AC: 3004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4013967; hg19: chr9-76897070;